From cb05c66b9e08503a59604d02204194ecf37bea2e Mon Sep 17 00:00:00 2001 From: John Major Date: Tue, 26 May 2026 16:19:01 -0700 Subject: [PATCH 01/47] Add Bloom container runtime --- .dockerignore | 16 + Dockerfile | 42 + bloom_lims/container_entry.py | 44 + container_tests/test_container_runtime.py | 56 + docker/entrypoint.sh | 16 + uv.lock | 2815 +++++++++++++++++++++ 6 files changed, 2989 insertions(+) create mode 100644 .dockerignore create mode 100644 Dockerfile create mode 100644 bloom_lims/container_entry.py create mode 100644 container_tests/test_container_runtime.py create mode 100755 docker/entrypoint.sh create mode 100644 uv.lock diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..bfaf8e3 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,16 @@ +.git +.mypy_cache +.pytest_cache +.ruff_cache +.venv +__pycache__ +*.py[cod] +build +dist +*.egg-info +.coverage +htmlcov +tests +docs/plans +analytics +stage_to_delete diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..046d925 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,42 @@ +# syntax=docker/dockerfile:1.7 +ARG PYTHON_VERSION=3.12 + +FROM ghcr.io/astral-sh/uv:0.5.30-python${PYTHON_VERSION}-bookworm-slim AS builder + +ARG SETUPTOOLS_SCM_PRETEND_VERSION=0.0.0 +ENV SETUPTOOLS_SCM_PRETEND_VERSION=${SETUPTOOLS_SCM_PRETEND_VERSION} \ + UV_COMPILE_BYTECODE=1 \ + UV_LINK_MODE=copy \ + PYTHONDONTWRITEBYTECODE=1 \ + PYTHONUNBUFFERED=1 + +WORKDIR /app +RUN apt-get update \ + && apt-get install -y --no-install-recommends build-essential libpq-dev \ + && rm -rf /var/lib/apt/lists/* +COPY pyproject.toml uv.lock README.md ./ +RUN uv sync --frozen --no-dev --no-install-project + +COPY bloom_lims ./bloom_lims +COPY main.py ./main.py +RUN uv sync --frozen --no-dev + +FROM python:${PYTHON_VERSION}-slim-bookworm AS runtime + +ENV PATH="/app/.venv/bin:${PATH}" \ + PYTHONDONTWRITEBYTECODE=1 \ + PYTHONUNBUFFERED=1 + +RUN addgroup --system lsmc && adduser --system --ingroup lsmc --home /app lsmc +WORKDIR /app +RUN apt-get update \ + && apt-get install -y --no-install-recommends libpq5 \ + && rm -rf /var/lib/apt/lists/* +COPY --from=builder --chown=lsmc:lsmc /app /app +COPY --chown=lsmc:lsmc docker/entrypoint.sh /entrypoint.sh +RUN chmod 0755 /entrypoint.sh +USER lsmc + +EXPOSE 8912 +ENTRYPOINT ["/entrypoint.sh"] +CMD ["python", "-m", "bloom_lims.container_entry"] diff --git a/bloom_lims/container_entry.py b/bloom_lims/container_entry.py new file mode 100644 index 0000000..4011afc --- /dev/null +++ b/bloom_lims/container_entry.py @@ -0,0 +1,44 @@ +"""Container foreground entrypoint for Bloom.""" + +from __future__ import annotations + +import os +from pathlib import Path + +def _required_env(name: str) -> str: + value = os.environ.get(name, "").strip() + if not value: + raise RuntimeError(f"{name} is required") + return value + + +def _required_absolute_file(name: str) -> Path: + path = Path(_required_env(name)) + if not path.is_absolute(): + raise RuntimeError(f"{name} must be an absolute path") + if not path.is_file(): + raise RuntimeError(f"{name} does not exist: {path}") + return path + + +def _start_server(**kwargs: object) -> None: + from bloom_lims.cli.server import start + + start(**kwargs) + + +def main() -> None: + _required_absolute_file("BLOOM_CONFIG_PATH") + _start_server( + port=int(_required_env("PORT")), + host=_required_env("HOST"), + reload=False, + background=False, + ssl=False, + cert=None, + key=None, + ) + + +if __name__ == "__main__": + main() diff --git a/container_tests/test_container_runtime.py b/container_tests/test_container_runtime.py new file mode 100644 index 0000000..4f93a29 --- /dev/null +++ b/container_tests/test_container_runtime.py @@ -0,0 +1,56 @@ +from __future__ import annotations + +from pathlib import Path +from unittest.mock import patch + +import pytest + +from bloom_lims import container_entry + + +PROJECT_ROOT = Path(__file__).resolve().parents[1] + + +def test_docker_runtime_files_use_foreground_uv_and_no_legacy_runtime() -> None: + dockerfile = (PROJECT_ROOT / "Dockerfile").read_text(encoding="utf-8") + entrypoint = (PROJECT_ROOT / "docker" / "entrypoint.sh").read_text(encoding="utf-8") + + assert "uv sync --frozen --no-dev --no-install-project" in dockerfile + assert "uv sync --frozen --no-dev" in dockerfile + assert "USER lsmc" in dockerfile + assert "python\", \"-m\", \"bloom_lims.container_entry" in dockerfile + assert ":latest" not in dockerfile + assert "conda" not in dockerfile.lower() + assert "tmux" not in entrypoint + assert "background" not in entrypoint + assert "${BLOOM_CONFIG_PATH:?BLOOM_CONFIG_PATH is required}" in entrypoint + + +def test_container_entry_requires_absolute_config_path(monkeypatch: pytest.MonkeyPatch) -> None: + monkeypatch.setenv("BLOOM_CONFIG_PATH", "relative.yaml") + + with pytest.raises(RuntimeError, match="must be an absolute path"): + container_entry._required_absolute_file("BLOOM_CONFIG_PATH") + + +def test_container_entry_runs_foreground_http_server( + tmp_path: Path, monkeypatch: pytest.MonkeyPatch +) -> None: + config_path = tmp_path / "bloom.yaml" + config_path.write_text("auth: {}\n", encoding="utf-8") + monkeypatch.setenv("BLOOM_CONFIG_PATH", str(config_path)) + monkeypatch.setenv("HOST", "127.0.0.1") + monkeypatch.setenv("PORT", "8912") + + with patch("bloom_lims.container_entry._start_server") as start: + container_entry.main() + + assert start.call_args.kwargs == { + "port": 8912, + "host": "127.0.0.1", + "reload": False, + "background": False, + "ssl": False, + "cert": None, + "key": None, + } diff --git a/docker/entrypoint.sh b/docker/entrypoint.sh new file mode 100755 index 0000000..e44ed84 --- /dev/null +++ b/docker/entrypoint.sh @@ -0,0 +1,16 @@ +#!/usr/bin/env sh +set -eu + +: "${LSMC_SERVICE_NAME:?LSMC_SERVICE_NAME is required}" +: "${LSMC_ENV:?LSMC_ENV is required}" +: "${LSMC_RUNTIME_CLASS:?LSMC_RUNTIME_CLASS is required}" +: "${BLOOM_CONFIG_PATH:?BLOOM_CONFIG_PATH is required}" +: "${HOST:?HOST is required}" +: "${PORT:?PORT is required}" +: "${OTEL_EXPORTER_OTLP_ENDPOINT:?OTEL_EXPORTER_OTLP_ENDPOINT is required}" + +export OTEL_SERVICE_NAME="${OTEL_SERVICE_NAME:-$LSMC_SERVICE_NAME}" +export OTEL_RESOURCE_ATTRIBUTES="service.name=${OTEL_SERVICE_NAME},deployment.environment=${LSMC_ENV},service.version=${LSMC_RELEASE_SHA:-unknown}" +export LOG_FORMAT="${LOG_FORMAT:-json}" + +exec "$@" diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..6a24122 --- /dev/null +++ b/uv.lock @@ -0,0 +1,2815 @@ +version = 1 +revision = 3 +requires-python = ">=3.12" +resolution-markers = [ + "python_full_version >= '3.15' and sys_platform == 'win32'", + "python_full_version >= '3.15' and sys_platform == 'emscripten'", + "python_full_version >= '3.15' and sys_platform != 'emscripten' and sys_platform != 'win32'", + "python_full_version == '3.14.*' and sys_platform == 'win32'", + "python_full_version == '3.14.*' and 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AGENTS.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/AGENTS.md b/AGENTS.md index 893ead6..b491752 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -1,3 +1,10 @@ +# Shell Session Defaults + +- Default to an interactive shell for shell work. On this Mac, use the user's default shell unless the user explicitly asks for another shell. +- For AWS EC2, ParallelCluster, and other remote Linux hosts, default to an interactive `bash` login shell as `ubuntu`. Do not use `root` unless the user explicitly grants permission for that specific work; use targeted `sudo` from `ubuntu` when escalation is required. +- For Daylily/DayOA/DAY-EC headnode workflow work, use an interactive `ubuntu` tmux/login-shell pane for controllers and workflow commands. Run setup as separate commands in that pane (`source dyoainit`, then `dy-a ...`, then `dy-r ...`) so aliases/functions are defined before use. +- SSM Run Command is for simple inspection or for writing helper scripts through the supported helpers. Do not launch workflow controllers or rely on `dy-*` aliases from non-interactive SSM scripts. + # Bloom CLI Policy ## Session Setup @@ -57,6 +64,16 @@ source ./activate - Service-host certs use DNS-01 renewal; do not depend on HTTP-01 public reachability for Bloom service hosts. - Future dev, test, and stage deployments must use their own approved-source lists, credentials, certificates, TapDB schemas, and tenant data, separate from production. +## Version Tags + +- Use non-v semver tags for package releases, e.g. `2.0.19` or `5.0.21`, not `v2.0.19`. +- Commit first, then tag the exact clean release commit. +- Use annotated tags for release provenance: `git tag -a 2.0.19 -m "Release 2.0.19"`. +- Lightweight tags are acceptable only for scratch/internal marks, not package releases. +- Do not move or overwrite pushed version tags. If a pushed tag is wrong, cut the next patch version. +- If signing is configured and expected, use signed annotated tags: `git tag -s 2.0.19 -m "Release 2.0.19"`. +- Verify tag type with `git cat-file -t 2.0.18`; `tag` means annotated and `commit` means lightweight. + ## Bloom Examples - Start with `source ./activate ` From 901d340d2b8d352e395261613551565ec284a697 Mon Sep 17 00:00:00 2001 From: John Major Date: Thu, 28 May 2026 14:14:57 -0700 Subject: [PATCH 03/47] Package Bloom TapDB templates in container image --- Dockerfile | 1 + tests/test_packaging_metadata.py | 10 +++++++++- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 046d925..875e66f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -17,6 +17,7 @@ RUN apt-get update \ COPY pyproject.toml uv.lock README.md ./ RUN uv sync --frozen --no-dev --no-install-project +COPY config ./config COPY bloom_lims ./bloom_lims COPY main.py ./main.py RUN uv sync --frozen --no-dev diff --git a/tests/test_packaging_metadata.py b/tests/test_packaging_metadata.py index ec4b740..0cf2482 100644 --- a/tests/test_packaging_metadata.py +++ b/tests/test_packaging_metadata.py @@ -15,9 +15,17 @@ def test_project_dependencies_pin_release_train_versions() -> None: assert "cli-core-yo==2.1.1" in dependencies assert "daylily-auth-cognito==2.1.5" in dependencies - assert "daylily-tapdb>=7.0.3,<8.0.0" in dependencies + assert "daylily-tapdb>=7.0.5,<8.0.0" in dependencies assert "IPython>=8.18.1" in dependencies assert "psycopg2==2.9.9" in dependencies assert not any(str(dep).startswith("zebra-day") for dep in dependencies) assert "djlint" in dependencies assert "optional-dependencies" not in data["project"] + + +def test_dockerfile_copies_tapdb_template_config() -> None: + dockerfile = (Path(__file__).resolve().parents[1] / "Dockerfile").read_text( + encoding="utf-8" + ) + + assert "COPY config ./config" in dockerfile From c7040467dd939f9d78fe16726b334b59d2abc2f4 Mon Sep 17 00:00:00 2001 From: John Major Date: Thu, 28 May 2026 14:46:02 -0700 Subject: [PATCH 04/47] Initialize Bloom container runtime context --- bloom_lims/container_entry.py | 29 +++++++++++++++++- tests/test_container_entry_runtime.py | 42 +++++++++++++++++++++++++++ 2 files changed, 70 insertions(+), 1 deletion(-) create mode 100644 tests/test_container_entry_runtime.py diff --git a/bloom_lims/container_entry.py b/bloom_lims/container_entry.py index 4011afc..657ff4b 100644 --- a/bloom_lims/container_entry.py +++ b/bloom_lims/container_entry.py @@ -5,6 +5,7 @@ import os from pathlib import Path + def _required_env(name: str) -> str: value = os.environ.get(name, "").strip() if not value: @@ -27,8 +28,34 @@ def _start_server(**kwargs: object) -> None: start(**kwargs) +def _initialize_runtime_context(config_path: Path) -> None: + from cli_core_yo.errors import ContextNotInitializedError + from cli_core_yo.runtime import get_context, initialize + from cli_core_yo.xdg import resolve_paths + + from bloom_lims.cli import spec + + try: + get_context() + return + except ContextNotInitializedError: + pass + + initialize( + spec, + resolve_paths(spec.xdg), + config_path=config_path, + invocation={"entrypoint": "container"}, + backend_name="container", + backend_kind="container", + runtime_guard_mode="off", + runtime_check_skipped=True, + ) + + def main() -> None: - _required_absolute_file("BLOOM_CONFIG_PATH") + config_path = _required_absolute_file("BLOOM_CONFIG_PATH") + _initialize_runtime_context(config_path) _start_server( port=int(_required_env("PORT")), host=_required_env("HOST"), diff --git a/tests/test_container_entry_runtime.py b/tests/test_container_entry_runtime.py new file mode 100644 index 0000000..00656b1 --- /dev/null +++ b/tests/test_container_entry_runtime.py @@ -0,0 +1,42 @@ +from __future__ import annotations + +from cli_core_yo import runtime as cli_runtime + + +def test_container_entry_initializes_cli_runtime(monkeypatch, tmp_path): + import bloom_lims.container_entry as entry + + config_path = tmp_path / "bloom.yaml" + config_path.write_text("application: {}\n", encoding="utf-8") + monkeypatch.setenv("BLOOM_CONFIG_PATH", str(config_path)) + monkeypatch.setenv("PORT", "8912") + monkeypatch.setenv("HOST", "0.0.0.0") + monkeypatch.setenv("DEPLOYMENT_CODE", "inf9") + monkeypatch.setenv("XDG_CONFIG_HOME", str(tmp_path / "xdg" / "config")) + monkeypatch.setenv("XDG_STATE_HOME", str(tmp_path / "xdg" / "state")) + monkeypatch.setenv("XDG_DATA_HOME", str(tmp_path / "xdg" / "data")) + monkeypatch.setenv("XDG_CACHE_HOME", str(tmp_path / "xdg" / "cache")) + + observed: dict[str, object] = {} + + def fake_start(**kwargs: object) -> None: + observed["kwargs"] = kwargs + observed["config_path"] = cli_runtime.get_context().config_path + + monkeypatch.setattr(entry, "_start_server", fake_start) + cli_runtime._reset() + try: + entry.main() + finally: + cli_runtime._reset() + + assert observed["config_path"] == config_path + assert observed["kwargs"] == { + "port": 8912, + "host": "0.0.0.0", + "reload": False, + "background": False, + "ssl": False, + "cert": None, + "key": None, + } From fcac343eb5eac33e910e2d20bc70a41c16d65674 Mon Sep 17 00:00:00 2001 From: John Major Date: Thu, 28 May 2026 15:09:04 -0700 Subject: [PATCH 05/47] Copy Bloom UI assets into container image --- Dockerfile | 2 ++ tests/test_packaging_metadata.py | 2 ++ 2 files changed, 4 insertions(+) diff --git a/Dockerfile b/Dockerfile index 875e66f..1aec54f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -20,6 +20,8 @@ RUN uv sync --frozen --no-dev --no-install-project COPY config ./config COPY bloom_lims ./bloom_lims COPY main.py ./main.py +COPY static ./static +COPY templates ./templates RUN uv sync --frozen --no-dev FROM python:${PYTHON_VERSION}-slim-bookworm AS runtime diff --git a/tests/test_packaging_metadata.py b/tests/test_packaging_metadata.py index 0cf2482..6213dd8 100644 --- a/tests/test_packaging_metadata.py +++ b/tests/test_packaging_metadata.py @@ -29,3 +29,5 @@ def test_dockerfile_copies_tapdb_template_config() -> None: ) assert "COPY config ./config" in dockerfile + assert "COPY static ./static" in dockerfile + assert "COPY templates ./templates" in dockerfile From e7caca9b9e41e9e49f19d3732553a3659a839e1e Mon Sep 17 00:00:00 2001 From: John Major Date: Fri, 29 May 2026 14:48:01 -0700 Subject: [PATCH 06/47] Standardize Bloom GUI auth entrypoints --- AGENTS.md | 6 ++++++ Dockerfile | 1 + bloom_lims/app.py | 11 +++-------- bloom_lims/gui/routes/auth.py | 4 ++-- bloom_lims/integrations/tapdb_mount.py | 10 +++++++++- pyproject.toml | 2 +- tests/test_deploy_contract.py | 8 ++++++++ tests/test_route_coverage_gaps_gui.py | 5 +---- tests/test_route_inventory_guard.py | 4 ++++ tests/test_tapdb_mount.py | 2 +- 10 files changed, 36 insertions(+), 17 deletions(-) diff --git a/AGENTS.md b/AGENTS.md index b491752..74472f0 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -81,3 +81,9 @@ source ./activate - Use `bloom db seed` - Use `bloom server start --port 8912` - Use `tapdb ...` and `daycog ...` only where Bloom docs or Bloom CLI explicitly delegate to them +# DEPLOYED SERVICE GUI AUTH EVIDENCE + +- For deployed service acceptance, API health checks and HTTP `302` redirects are not sufficient. Also use Playwright or the bundled Playwright CLI workflow to open each deployed GUI login page, snapshot the page, click through to the Google OAuth option, and capture screenshots. +- Store screenshots and records under `output/playwright/` or the deployment ledger evidence directory. Record service name, deploy name, URL, timestamp, screenshot paths, and status as `confirmed_success` or `confirmed_fail`. +- If the Google OAuth click reaches an expected external blocker, such as `redirect_uri_mismatch`, record the exact callback URI and mark the row blocked instead of treating the service as healthy. +- Debug and fix failures that are in repository/deployment scope. If the failure requires external configuration or human credentials, annotate the reason precisely. Do not enter real user credentials unless the user explicitly authorizes that in the current turn. diff --git a/Dockerfile b/Dockerfile index 1aec54f..bda0787 100644 --- a/Dockerfile +++ b/Dockerfile @@ -18,6 +18,7 @@ COPY pyproject.toml uv.lock README.md ./ RUN uv sync --frozen --no-dev --no-install-project COPY config ./config +COPY auth ./auth COPY bloom_lims ./bloom_lims COPY main.py ./main.py COPY static ./static diff --git a/bloom_lims/app.py b/bloom_lims/app.py index d7eb2f0..5fb5d86 100644 --- a/bloom_lims/app.py +++ b/bloom_lims/app.py @@ -193,14 +193,9 @@ async def _enforce_origin_allowlist(request, call_next): app.include_router(probe_router) app.include_router(observability_router) app.include_router(api_v1_router) - try: - from bloom_lims.gui.router import router as gui_router - except ModuleNotFoundError as exc: - logging.warning( - "Skipping GUI router due to missing optional dependency: %s", exc.name - ) - else: - app.include_router(gui_router) + from bloom_lims.gui.router import router as gui_router + + app.include_router(gui_router) register_exception_handlers(app) return app diff --git a/bloom_lims/gui/routes/auth.py b/bloom_lims/gui/routes/auth.py index a93a3ea..2c9165a 100644 --- a/bloom_lims/gui/routes/auth.py +++ b/bloom_lims/gui/routes/auth.py @@ -788,5 +788,5 @@ async def auth_logout_post(request: Request, response: Response): @router.get("/logout") -async def logout(request: Request, response: Response): - return await _logout_response(request, response) +async def logout(): + return RedirectResponse(url="/auth/logout", status_code=status.HTTP_303_SEE_OTHER) diff --git a/bloom_lims/integrations/tapdb_mount.py b/bloom_lims/integrations/tapdb_mount.py index f5a3e02..e44e0b8 100644 --- a/bloom_lims/integrations/tapdb_mount.py +++ b/bloom_lims/integrations/tapdb_mount.py @@ -8,6 +8,7 @@ from dataclasses import dataclass from pathlib import Path from typing import Any, Awaitable, Callable +from urllib.parse import quote from fastapi import FastAPI from starlette.datastructures import Headers @@ -143,7 +144,14 @@ async def __call__( content={"detail": "Authentication required"}, ) else: - response = RedirectResponse(url="/login", status_code=303) + next_path = str(scope.get("path") or "/") + query_string = scope.get("query_string") or b"" + if query_string: + next_path = f"{next_path}?{query_string.decode('utf-8', errors='ignore')}" + response = RedirectResponse( + url=f"/login?next={quote(next_path, safe='/')}", + status_code=303, + ) await response(scope, receive, send) return diff --git a/pyproject.toml b/pyproject.toml index bad3528..65559a0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -91,7 +91,7 @@ version_file = "bloom_lims/_scm_version.py" [tool.setuptools.packages.find] where = ["."] -include = ["bloom_lims*"] +include = ["auth*", "bloom_lims*"] [tool.setuptools.package-data] bloom_lims = ["etc/*.yaml", "etc/*.json"] diff --git a/tests/test_deploy_contract.py b/tests/test_deploy_contract.py index baf5d85..5701efe 100644 --- a/tests/test_deploy_contract.py +++ b/tests/test_deploy_contract.py @@ -43,3 +43,11 @@ def test_db_build_help_mentions_target_option() -> None: result = runner.invoke(build_app(), ["db", "build", "--help"]) assert result.exit_code == 0 assert "--target" in result.output + + +def test_container_packages_gui_auth_module() -> None: + dockerfile = (PROJECT_ROOT / "Dockerfile").read_text(encoding="utf-8") + pyproject = (PROJECT_ROOT / "pyproject.toml").read_text(encoding="utf-8") + + assert "COPY auth ./auth" in dockerfile + assert '"auth*"' in pyproject diff --git a/tests/test_route_coverage_gaps_gui.py b/tests/test_route_coverage_gaps_gui.py index 710123d..7829a83 100644 --- a/tests/test_route_coverage_gaps_gui.py +++ b/tests/test_route_coverage_gaps_gui.py @@ -349,7 +349,4 @@ def test_logout_alias_routes_execute_handler_body(client: TestClient) -> None: logout = client.get("/logout", follow_redirects=False) assert logout.status_code == 303 - assert ( - logout.headers["location"] - == "https://example.auth.us-west-2.amazoncognito.com/logout" - ) + assert logout.headers["location"] == "/auth/logout" diff --git a/tests/test_route_inventory_guard.py b/tests/test_route_inventory_guard.py index f912ea5..8633583 100644 --- a/tests/test_route_inventory_guard.py +++ b/tests/test_route_inventory_guard.py @@ -89,6 +89,10 @@ def _iter_runtime_routes() -> set[tuple[str, str]]: def test_docs_routes_remain_enabled_and_render(client: TestClient) -> None: + root = client.get("/", follow_redirects=False) + assert root.status_code in {200, 302, 303, 307, 308} + assert root.status_code != 404 + openapi = client.get("/openapi.json") assert openapi.status_code == 200 assert openapi.json()["openapi"].startswith("3.") diff --git a/tests/test_tapdb_mount.py b/tests/test_tapdb_mount.py index edd0f36..29ffc7a 100644 --- a/tests/test_tapdb_mount.py +++ b/tests/test_tapdb_mount.py @@ -29,7 +29,7 @@ def test_unauthenticated_request_redirects_to_bloom_login(): with _client() as client: response = client.get("/admin/tapdb/login", follow_redirects=False) assert response.status_code == 303 - assert response.headers.get("location") == "/login" + assert response.headers.get("location") == "/login?next=/admin/tapdb/login" json_response = client.get( "/admin/tapdb/login", From 896569bbec267be573bd566ad1ec5e673c3843b5 Mon Sep 17 00:00:00 2001 From: John Major Date: Mon, 1 Jun 2026 13:10:37 -0700 Subject: [PATCH 07/47] Restore Bloom prefix taxonomy templates --- README.md | 59 + bloom_lims/domain/beta_lab.py | 20 +- bloom_lims/domain/beta_lab_stages.py | 38 +- bloom_lims/domain/beta_lab_store.py | 10 +- bloom_lims/domain/execution_queue.py | 20 +- bloom_lims/etc/prefix_ownership_registry.json | 120 + bloom_lims/schemas/beta_lab.py | 25 +- config/tapdb_templates/bloom/templates.json | 4100 ++++++++++++++++- tests/test_bloom_prefix_taxonomy.py | 162 + tests/test_queue_flow.py | 24 +- tests/test_sequencing_run_contract.py | 48 +- 11 files changed, 4486 insertions(+), 140 deletions(-) create mode 100644 tests/test_bloom_prefix_taxonomy.py diff --git a/README.md b/README.md index 0037720..7b9a562 100644 --- a/README.md +++ b/README.md @@ -226,6 +226,65 @@ curl -k https://localhost:8912/api/v1/external/specimens \ Deep dive: [docs/apis.md](docs/apis.md) +## Prefix Taxonomy + +Bloom EUID prefixes are governed display labels for operators and downstream +records. Prefixes are governance and display labels only; they do not drive +behavior, authorization, routing, template lookup, or workflow dispatch. Code +should use explicit template codes and semantic properties for behavior. + +| Family | Meaning | +| --- | --- | +| `BC*` | Containers | +| `BN*` | Contents, materials, and reagents | +| `BD*` | Data and evidence objects | +| `BR*` | Runs and executions | +| `BG*` | Generic helpers and external-object mappings | + +Concrete template kinds use three-letter prefixes. Two-letter prefixes are +generic class reserves only: `BC`, `BN`, `BD`, `BR`, and `BG`. New Bloom-owned +prefixes must not contain `I`, `L`, `O`, or `U`, and explicit numeric EUID +input must not use leading zeros. + +Current concrete wet-lab prefixes: + +| Template kind | Category | Prefix | +| --- | --- | --- | +| tube container | `container` | `BCT` | +| plate container | `container` | `BCP` | +| well container | `container` | `BCW` | +| bottle container | `container` | `BCB` | +| flowcell container | `container` | `BCF` | +| flowcell lane container | `container` | `BCE` | +| rack, box, or storage container | `container` | `BCR` | +| blood specimen/content | `content` | `BNB` | +| buccal specimen content | `content` | `BNS` | +| saliva specimen content | `content` | `BNA` | +| gDNA content | `content` | `BNG` | +| cfDNA content | `content` | `BNC` | +| sequencing library content | `content` | `BNQ` | +| sequencing library pool content | `content` | `BNP` | +| generic reagent content | `content` | `BNR` | +| sequencing index reagent content | `content` | `BNX` | +| control material content | `content` | `BNK` | +| gDNA quantification data | `data` | `BDQ` | +| extraction run evidence/data | `data` | `BDX` | +| extraction QC run evidence/data | `data` | `BDY` | +| library prep run evidence/data | `data` | `BDP` | +| pooling run evidence/data | `data` | `BDN` | +| library-index assignment data | `data` | `BDA` | +| transfer execution data | `data` | `BDT` | +| Illumina sequencing run | `run` | `BRM` | +| ONT sequencing run | `run` | `BRN` | +| Ultima sequencing run | `run` | `BRT` | +| PacBio sequencing run | `run` | `BRP` | +| Complete Genomics sequencing run | `run` | `BRC` | +| external object mapping | `generic` | `BGX` | + +Invalid historical proposals are explicitly replaced: `BCL` becomes `BCE`, +`BRI` becomes `BRM`, `BRO` becomes `BRN`, `BRU` becomes `BRT`, `BNL` becomes +`BNQ`, and `BDL` becomes `BDP`. Existing historical objects keep their already minted EUIDs; template prefix changes only affect future object creation. + ## GUI Overview Bloom's GUI is an operator and developer surface, not just a demo shell. The main current routes are: diff --git a/bloom_lims/domain/beta_lab.py b/bloom_lims/domain/beta_lab.py index 295d3dd..1c1a4b4 100644 --- a/bloom_lims/domain/beta_lab.py +++ b/bloom_lims/domain/beta_lab.py @@ -35,6 +35,15 @@ class BetaLabService( ORGANIZATION_SITE_REFERENCE_TYPE = "atlas_organization_site" COLLECTION_EVENT_REFERENCE_TYPE = "atlas_collection_event" GENERIC_DATA_TEMPLATE_CODE = "data/generic/generic/1.0" + DATA_TEMPLATE_BY_BETA_KIND = { + "extraction_batch": "data/operation/extraction/1.0", + "extraction_run": "data/operation/extraction/1.0", + "post_extract_qc_result": "data/operation/extraction-qc/1.0", + "library_qc_result": "data/operation/library-prep/1.0", + "pooling_run": "data/operation/pooling/1.0", + "sequenced_library_assignment": "data/library-index-assignment/sequencing-library/1.0", + "run_artifact": "data/execution/transfer/1.0", + } BETA_KIND_QUEUE_DEFINITION = "queue_definition" BETA_KIND_QUEUE_EVENT = "queue_event" BETA_KIND_WORK_ITEM = "beta_work_item" @@ -51,15 +60,18 @@ class BetaLabService( REL_MATERIAL_CONSUMPTION = "beta_material_consumption" REL_USED_INSTRUMENT = "beta_used_instrument" REL_USED_REAGENT = "beta_used_reagent" - POOL_TEMPLATE_CODE = "content/pool/generic/1.0" + POOL_TEMPLATE_CODE = "content/pool/sequencing-library/1.0" POOL_CONTAINER_TEMPLATE_CODE = "container/tube/tube-generic-10ml/1.0" - LIBRARY_PREP_OUTPUT_TEMPLATE_CODE = "data/wetlab/library_prep_output/1.0" + LIBRARY_PREP_OUTPUT_TEMPLATE_CODE = "data/operation/library-prep/1.0" + LIBRARY_MATERIAL_TEMPLATE_CODE = "content/sample/sequencing-library/1.0" SEQUENCING_RUN_TEMPLATE_BY_SUBTYPE = { "illumina": "data/sequencing_run/illumina/1.0", "ont": "data/sequencing_run/ont/1.0", - "novaseq": "data/sequencing_run/novaseq/1.0", + "ultima": "data/sequencing_run/ultima/1.0", + "pacbio": "data/sequencing_run/pacbio/1.0", + "completegenomics": "data/sequencing_run/completegenomics/1.0", } - LIBRARY_PLATE_TEMPLATE_CODE = "container/plate/fixed-plate-96/1.0" + LIBRARY_PLATE_TEMPLATE_CODE = "container/plate/sequencing-library-plate-96/1.0" EXTRACTION_TEMPLATE_BY_TYPE = { "cfdna": "content/sample/cfdna/1.0", "gdna": "content/sample/gdna/1.0", diff --git a/bloom_lims/domain/beta_lab_stages.py b/bloom_lims/domain/beta_lab_stages.py index 9d927fe..ae620b1 100644 --- a/bloom_lims/domain/beta_lab_stages.py +++ b/bloom_lims/domain/beta_lab_stages.py @@ -61,6 +61,7 @@ def _resolve_or_create_stage_data_record( "idempotency_key": record_idempotency_key, "occurred_at": self._timestamp(), }, + template_code=self.DATA_TEMPLATE_BY_BETA_KIND.get(beta_kind), ) def create_extraction( @@ -388,6 +389,9 @@ def record_post_extract_qc( "idempotency_key": idempotency_key or "", "occurred_at": self._timestamp(), }, + template_code=self.DATA_TEMPLATE_BY_BETA_KIND.get( + "post_extract_qc_result" + ), ) if payload.quant_artifact_euid: qc_props = self._props(qc_record) @@ -627,14 +631,13 @@ def create_library_prep( str(self._props(source).get("extraction_type") or "gdna").strip().lower() ) library_material = self.bobj.create_instance_by_code( - self.EXTRACTION_TEMPLATE_BY_TYPE.get( - extraction_type, "content/sample/gdna/1.0" - ), + self.LIBRARY_MATERIAL_TEMPLATE_CODE, { "json_addl": { "properties": { "beta_kind": "library_material", "platform": payload.platform, + "source_extraction_type": extraction_type, "idempotency_key": idempotency_key or "", "metadata": normalized_metadata, } @@ -843,6 +846,7 @@ def record_library_qc( "idempotency_key": idempotency_key or "", "occurred_at": self._timestamp(), }, + template_code=self.DATA_TEMPLATE_BY_BETA_KIND.get("library_qc_result"), ) self.bobj.create_generic_instance_lineage_by_euids( library_material.euid, @@ -980,6 +984,24 @@ def create_pool( pool.name = pool_name pool_props["name"] = pool_name self._write_props(pool, pool_props) + pooling_run = self._create_data_record( + beta_kind="pooling_run", + name=f"pooling:{pool.euid}", + properties={ + "platform": payload.platform, + "member_euids": [member.euid for member in members], + "pool_euid": pool.euid, + "metadata": normalized_metadata, + "idempotency_key": idempotency_key or "", + "occurred_at": self._timestamp(), + }, + template_code=self.DATA_TEMPLATE_BY_BETA_KIND.get("pooling_run"), + ) + self.bobj.create_generic_instance_lineage_by_euids( + pooling_run.euid, + pool.euid, + relationship_type="beta_pooling_run_output", + ) pool_container = self.bobj.create_instance_by_code( payload.pool_container_template_code or self.POOL_CONTAINER_TEMPLATE_CODE, @@ -996,6 +1018,11 @@ def create_pool( pool.euid, relationship_type="beta_pool_member", ) + self.bobj.create_generic_instance_lineage_by_euids( + member.euid, + pooling_run.euid, + relationship_type="beta_pooling_run_input", + ) self._write_graph_metadata( pool, node_role="sequencing_pool", @@ -1065,6 +1092,7 @@ def create_pool( result={ "status": "success", "pool_euid": pool.euid, + "pooling_run_euid": pooling_run.euid, "pool_container_euid": pool_container.euid, "current_queue": self.START_RUN_QUEUE_BY_PLATFORM[payload.platform], "member_count": len(members), @@ -1229,6 +1257,9 @@ def create_run( "library_material_euid": assignment.library_material_euid or "", "barcode_reagent_euid": assignment.barcode_reagent_euid or "", }, + template_code=self.DATA_TEMPLATE_BY_BETA_KIND.get( + "sequenced_library_assignment" + ), ) self.bobj.create_generic_instance_lineage_by_euids( run.euid, @@ -1310,6 +1341,7 @@ def create_run( "s3_uri": s3_uri, "dewey_artifact_euid": dewey_artifact_euid or "", }, + template_code=self.DATA_TEMPLATE_BY_BETA_KIND.get("run_artifact"), ) self.bobj.create_generic_instance_lineage_by_euids( run.euid, diff --git a/bloom_lims/domain/beta_lab_store.py b/bloom_lims/domain/beta_lab_store.py index 91b3bf7..a4381a9 100644 --- a/bloom_lims/domain/beta_lab_store.py +++ b/bloom_lims/domain/beta_lab_store.py @@ -293,8 +293,14 @@ def _ensure_fixed_container_graph_metadata(self, instance) -> None: return type_name = str(instance.type or "").strip() subtype = str(instance.subtype or "").strip() - if type_name == "plate" and subtype in {"fixed-plate-96", "fixed-plate-24"}: - max_wells = 96 if subtype == "fixed-plate-96" else 24 + plate_well_counts = { + "fixed-plate-24": 24, + "fixed-plate-96": 96, + "index-plate-96": 96, + "sequencing-library-plate-96": 96, + } + if type_name == "plate" and subtype in plate_well_counts: + max_wells = plate_well_counts[subtype] self._write_graph_metadata( instance, node_role=subtype, diff --git a/bloom_lims/domain/execution_queue.py b/bloom_lims/domain/execution_queue.py index febf736..7d7e038 100644 --- a/bloom_lims/domain/execution_queue.py +++ b/bloom_lims/domain/execution_queue.py @@ -165,8 +165,7 @@ class ExecutionQueueService: "display_name": "Illumina Library QC", "dispatch_priority": 100, "subject_template_codes": [ - "content/sample/cfdna/1.0", - "content/sample/gdna/1.0", + "content/sample/sequencing-library/1.0", ], "required_worker_capabilities": ["wetlab.library_qc", "platform.ILMN"], }, @@ -183,9 +182,8 @@ class ExecutionQueueService: "display_name": "Illumina Sequencing Pool", "dispatch_priority": 100, "subject_template_codes": [ - "data/wetlab/library_prep_output/1.0", - "content/sample/cfdna/1.0", - "content/sample/gdna/1.0", + "data/operation/library-prep/1.0", + "content/sample/sequencing-library/1.0", ], "required_worker_capabilities": ["wetlab.pooling", "platform.ILMN"], }, @@ -193,22 +191,21 @@ class ExecutionQueueService: "display_name": "ONT Sequencing Pool", "dispatch_priority": 100, "subject_template_codes": [ - "data/wetlab/library_prep_output/1.0", - "content/sample/cfdna/1.0", - "content/sample/gdna/1.0", + "data/operation/library-prep/1.0", + "content/sample/sequencing-library/1.0", ], "required_worker_capabilities": ["wetlab.pooling", "platform.ONT"], }, "ilmn_start_seq_run": { "display_name": "Illumina Start Run", "dispatch_priority": 100, - "subject_template_codes": ["content/pool/generic/1.0"], + "subject_template_codes": ["content/pool/sequencing-library/1.0"], "required_worker_capabilities": ["wetlab.run_start", "platform.ILMN"], }, "ont_start_seq_run": { "display_name": "ONT Start Run", "dispatch_priority": 100, - "subject_template_codes": ["content/pool/generic/1.0"], + "subject_template_codes": ["content/pool/sequencing-library/1.0"], "required_worker_capabilities": ["wetlab.run_start", "platform.ONT"], }, "post_extract_exception": { @@ -224,8 +221,7 @@ class ExecutionQueueService: "display_name": "Illumina Library QC Exception", "dispatch_priority": 10, "subject_template_codes": [ - "content/sample/cfdna/1.0", - "content/sample/gdna/1.0", + "content/sample/sequencing-library/1.0", ], "required_worker_capabilities": [ "wetlab.exception_review", diff --git a/bloom_lims/etc/prefix_ownership_registry.json b/bloom_lims/etc/prefix_ownership_registry.json index 43581fc..f187f31 100644 --- a/bloom_lims/etc/prefix_ownership_registry.json +++ b/bloom_lims/etc/prefix_ownership_registry.json @@ -13,27 +13,147 @@ "BBX": { "issuer_app_code": "bloom" }, + "BC": { + "issuer_app_code": "bloom" + }, + "BCB": { + "issuer_app_code": "bloom" + }, + "BCE": { + "issuer_app_code": "bloom" + }, + "BCF": { + "issuer_app_code": "bloom" + }, "BCN": { "issuer_app_code": "bloom" }, + "BCP": { + "issuer_app_code": "bloom" + }, + "BCR": { + "issuer_app_code": "bloom" + }, "BCT": { "issuer_app_code": "bloom" }, + "BCW": { + "issuer_app_code": "bloom" + }, + "BD": { + "issuer_app_code": "bloom" + }, + "BDA": { + "issuer_app_code": "bloom" + }, + "BDC": { + "issuer_app_code": "bloom" + }, + "BDN": { + "issuer_app_code": "bloom" + }, + "BDP": { + "issuer_app_code": "bloom" + }, + "BDQ": { + "issuer_app_code": "bloom" + }, "BDT": { "issuer_app_code": "bloom" }, + "BDX": { + "issuer_app_code": "bloom" + }, + "BDY": { + "issuer_app_code": "bloom" + }, "BEQ": { "issuer_app_code": "bloom" }, "BFX": { "issuer_app_code": "bloom" }, + "BG": { + "issuer_app_code": "bloom" + }, + "BGM": { + "issuer_app_code": "bloom" + }, + "BGP": { + "issuer_app_code": "bloom" + }, + "BGR": { + "issuer_app_code": "bloom" + }, + "BGS": { + "issuer_app_code": "bloom" + }, "BGT": { "issuer_app_code": "bloom" }, + "BGV": { + "issuer_app_code": "bloom" + }, + "BGX": { + "issuer_app_code": "bloom" + }, "BHE": { "issuer_app_code": "bloom" }, + "BN": { + "issuer_app_code": "bloom" + }, + "BNA": { + "issuer_app_code": "bloom" + }, + "BNB": { + "issuer_app_code": "bloom" + }, + "BNC": { + "issuer_app_code": "bloom" + }, + "BNF": { + "issuer_app_code": "bloom" + }, + "BNG": { + "issuer_app_code": "bloom" + }, + "BNK": { + "issuer_app_code": "bloom" + }, + "BNP": { + "issuer_app_code": "bloom" + }, + "BNQ": { + "issuer_app_code": "bloom" + }, + "BNR": { + "issuer_app_code": "bloom" + }, + "BNS": { + "issuer_app_code": "bloom" + }, + "BNX": { + "issuer_app_code": "bloom" + }, + "BR": { + "issuer_app_code": "bloom" + }, + "BRC": { + "issuer_app_code": "bloom" + }, + "BRM": { + "issuer_app_code": "bloom" + }, + "BRN": { + "issuer_app_code": "bloom" + }, + "BRP": { + "issuer_app_code": "bloom" + }, + "BRT": { + "issuer_app_code": "bloom" + }, "BSJ": { "issuer_app_code": "bloom" }, diff --git a/bloom_lims/schemas/beta_lab.py b/bloom_lims/schemas/beta_lab.py index d6ca59f..ea589d6 100644 --- a/bloom_lims/schemas/beta_lab.py +++ b/bloom_lims/schemas/beta_lab.py @@ -347,8 +347,10 @@ class BetaRunArtifactInput(BaseModel): class BetaRunCreateRequest(BaseModel): pool_euid: str - platform: Literal["ILMN", "ONT"] - run_subtype: Literal["illumina", "ont", "novaseq"] = Field(default="illumina") + platform: Literal["ILMN", "ONT", "Ultima", "PacBio", "CompleteGenomics"] + run_subtype: Literal[ + "illumina", "ont", "ultima", "pacbio", "completegenomics" + ] = Field(default="illumina") flowcell_id: str run_name: str | None = None status: Literal["started", "completed"] = Field(default="completed") @@ -367,13 +369,18 @@ def validate_assignments(self) -> "BetaRunCreateRequest": raise ValueError("flowcell_id must not be empty") if not self.assignments: raise ValueError("assignments must not be empty") - if self.platform == "ONT" and self.run_subtype != "ont": - raise ValueError("platform=ONT requires run_subtype=ont") - if self.platform == "ILMN" and self.run_subtype not in { - "illumina", - "novaseq", - }: - raise ValueError("platform=ILMN requires run_subtype=illumina or novaseq") + expected_subtype_by_platform = { + "ILMN": "illumina", + "ONT": "ont", + "Ultima": "ultima", + "PacBio": "pacbio", + "CompleteGenomics": "completegenomics", + } + expected_subtype = expected_subtype_by_platform[self.platform] + if self.run_subtype != expected_subtype: + raise ValueError( + f"platform={self.platform} requires run_subtype={expected_subtype}" + ) if self.instrument_euid is not None and not self.instrument_euid.strip(): raise ValueError("instrument_euid must not be empty when provided") for field_name in ("operator_start_datetime", "sequencing_end_datetime"): diff --git a/config/tapdb_templates/bloom/templates.json b/config/tapdb_templates/bloom/templates.json index fc7edf2..c6feaaa 100644 --- a/config/tapdb_templates/bloom/templates.json +++ b/config/tapdb_templates/bloom/templates.json @@ -2701,11 +2701,11 @@ { "name": "Generic External Object Link", "polymorphic_discriminator": "generic_template", - "category": "BGT", + "category": "BGX", "type": "generic", "subtype": "external_object_link", "version": "1.0", - "instance_prefix": "BGT", + "instance_prefix": "BGX", "instance_polymorphic_identity": "generic_instance", "bstatus": "active", "is_singleton": false, @@ -2759,11 +2759,11 @@ { "name": "24 fixed well plate", "polymorphic_discriminator": "container_template", - "category": "BCN", + "category": "BCP", "type": "plate", "subtype": "fixed-plate-24", "version": "1.0", - "instance_prefix": "BCN", + "instance_prefix": "BCP", "instance_polymorphic_identity": "container_instance", "bstatus": "active", "is_singleton": false, @@ -3300,11 +3300,11 @@ { "name": "96 well fixed plate", "polymorphic_discriminator": "container_template", - "category": "BCN", + "category": "BCP", "type": "plate", "subtype": "fixed-plate-96", "version": "1.0", - "instance_prefix": "BCN", + "instance_prefix": "BCP", "instance_polymorphic_identity": "container_instance", "bstatus": "active", "is_singleton": false, @@ -4934,11 +4934,11 @@ { "name": "4 position Rack", "polymorphic_discriminator": "container_template", - "category": "BCN", + "category": "BCR", "type": "rack", "subtype": "tube-rack-4-empty", "version": "1.0", - "instance_prefix": "BCN", + "instance_prefix": "BCR", "instance_polymorphic_identity": "container_instance", "bstatus": "active", "is_singleton": false, @@ -4987,11 +4987,11 @@ { "name": "4 position Rack", "polymorphic_discriminator": "container_template", - "category": "BCN", + "category": "BCR", "type": "rack", "subtype": "tube-rack-generic", "version": "1.0", - "instance_prefix": "BCN", + "instance_prefix": "BCR", "instance_polymorphic_identity": "container_instance", "bstatus": "active", "is_singleton": false, @@ -5094,11 +5094,11 @@ { "name": "Shelf", "polymorphic_discriminator": "container_template", - "category": "BCN", + "category": "BCR", "type": "shelf", "subtype": "generic", "version": "1.0", - "instance_prefix": "BCN", + "instance_prefix": "BCR", "instance_polymorphic_identity": "container_instance", "bstatus": "active", "is_singleton": false, @@ -5150,11 +5150,11 @@ { "name": "10ml glass tube", "polymorphic_discriminator": "container_template", - "category": "BCN", + "category": "BCT", "type": "tube", "subtype": "tube-10ml-glass", "version": "1.0", - "instance_prefix": "BCN", + "instance_prefix": "BCT", "instance_polymorphic_identity": "container_instance", "bstatus": "active", "is_singleton": false, @@ -5206,11 +5206,11 @@ { "name": "1.5ml eppi tube", "polymorphic_discriminator": "container_template", - "category": "BCN", + "category": "BCT", "type": "tube", "subtype": "tube-eppi-1.5ml", "version": "1.0", - "instance_prefix": "BCN", + "instance_prefix": "BCT", "instance_polymorphic_identity": "container_instance", "bstatus": "active", "is_singleton": false, @@ -5262,11 +5262,11 @@ { "name": "Generic 10ml tube", "polymorphic_discriminator": "container_template", - "category": "BCN", + "category": "BCT", "type": "tube", "subtype": "tube-generic-10ml", "version": "1.0", - "instance_prefix": "BCN", + "instance_prefix": "BCT", "instance_polymorphic_identity": "container_instance", "bstatus": "active", "is_singleton": false, @@ -5318,11 +5318,11 @@ { "name": "strek 10ml", "polymorphic_discriminator": "container_template", - "category": "BCN", + "category": "BCT", "type": "tube", "subtype": "tube-strek-10ml", "version": "1.0", - "instance_prefix": "BCN", + "instance_prefix": "BCT", "instance_polymorphic_identity": "container_instance", "bstatus": "active", "is_singleton": false, @@ -5375,11 +5375,11 @@ { "name": "Mawi DNA Technologies - ISD-T-250 - iSWAB DNA Collection Tube - Buccal", "polymorphic_discriminator": "container_template", - "category": "BCN", + "category": "BCT", "type": "tube", "subtype": "mawi-isd-t-250-iswab-dna-collection-tube-buccal", "version": "1.0", - "instance_prefix": "BCN", + "instance_prefix": "BCT", "instance_polymorphic_identity": "container_instance", "bstatus": "active", "is_singleton": false, @@ -5435,11 +5435,11 @@ { "name": "plate well - fixed", "polymorphic_discriminator": "container_template", - "category": "BCN", + "category": "BCW", "type": "well", "subtype": "fixed-plate-well", "version": "1.0", - "instance_prefix": "BCN", + "instance_prefix": "BCW", "instance_polymorphic_identity": "container_instance", "bstatus": "active", "is_singleton": false, @@ -5490,11 +5490,11 @@ { "name": "giab NA12878", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNK", "type": "control", "subtype": "giab-HG001", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNK", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5534,11 +5534,11 @@ { "name": "giab NA24385", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNK", "type": "control", "subtype": "giab-HG002", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNK", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5578,11 +5578,11 @@ { "name": "synthetic-cfdna", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNK", "type": "control", "subtype": "synthetic-cfdna", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNK", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5622,11 +5622,11 @@ { "name": "NTC - water", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNK", "type": "control", "subtype": "water-ntc", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNK", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5666,11 +5666,11 @@ { "name": "Pool of Contents", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNP", "type": "pool", "subtype": "generic", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNP", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5702,11 +5702,11 @@ { "name": "Novaseq sequencing kit", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNR", "type": "reagent", "subtype": "ILMN-nova-seq-kit", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNR", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5745,11 +5745,11 @@ { "name": "idt probes for rare mendelian disease, v1.0", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNR", "type": "reagent", "subtype": "idt-probes-rare-mendelian", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNR", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5788,11 +5788,11 @@ { "name": "NaOH", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNR", "type": "reagent", "subtype": "naoh", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNR", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5832,11 +5832,11 @@ { "name": "plasma (whole blood)", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNB", "type": "sample", "subtype": "blood-plasma", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNB", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5870,11 +5870,11 @@ { "name": "cell free DNA ", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNC", "type": "sample", "subtype": "cfdna", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNC", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5908,11 +5908,11 @@ { "name": "genomic DNA", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNG", "type": "sample", "subtype": "gdna", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNG", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5946,11 +5946,11 @@ { "name": "Whole Blood", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNB", "type": "specimen", "subtype": "blood-whole", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNB", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -5984,11 +5984,11 @@ { "name": "Buccal Swab", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNS", "type": "specimen", "subtype": "buccal-swab", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNS", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -6022,11 +6022,11 @@ { "name": "FFPE Block", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNF", "type": "specimen", "subtype": "ffpe-block", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNF", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -6060,11 +6060,11 @@ { "name": "FFPE Slides", "polymorphic_discriminator": "content_template", - "category": "BCT", + "category": "BNF", "type": "specimen", "subtype": "ffpe-slice", "version": "1.0", - "instance_prefix": "BCT", + "instance_prefix": "BNF", "instance_polymorphic_identity": "content_instance", "bstatus": "active", "is_singleton": false, @@ -6335,11 +6335,11 @@ { "name": "Generic Data Record", "polymorphic_discriminator": "data_template", - "category": "BDT", + "category": "BD", "type": "generic", "subtype": "generic", "version": "1.0", - "instance_prefix": "BDT", + "instance_prefix": "BD", "instance_polymorphic_identity": "data_instance", "bstatus": "active", "is_singleton": false, @@ -6365,11 +6365,11 @@ { "name": "DNA Quant Data", "polymorphic_discriminator": "data_template", - "category": "BDT", + "category": "BDQ", "type": "generic", "subtype": "gdna-quantification", "version": "1.0", - "instance_prefix": "BDT", + "instance_prefix": "BDQ", "instance_polymorphic_identity": "data_instance", "bstatus": "active", "is_singleton": false, @@ -6408,11 +6408,11 @@ { "name": "Temperature Log Data", "polymorphic_discriminator": "data_template", - "category": "BDT", + "category": "BDC", "type": "generic", "subtype": "temperature-log", "version": "1.0", - "instance_prefix": "BDT", + "instance_prefix": "BDC", "instance_polymorphic_identity": "data_instance", "bstatus": "active", "is_singleton": false, @@ -6445,11 +6445,11 @@ { "name": "Wet-Lab Library Prep Output", "polymorphic_discriminator": "data_template", - "category": "BDT", + "category": "BDP", "type": "wetlab", "subtype": "library_prep_output", "version": "1.0", - "instance_prefix": "BDT", + "instance_prefix": "BDP", "instance_polymorphic_identity": "data_instance", "bstatus": "active", "is_singleton": false, @@ -6478,11 +6478,11 @@ { "name": "Illumina Sequencing Run", "polymorphic_discriminator": "data_template", - "category": "BDT", + "category": "BRM", "type": "sequencing_run", "subtype": "illumina", "version": "1.0", - "instance_prefix": "BDT", + "instance_prefix": "BRM", "instance_polymorphic_identity": "data_instance", "bstatus": "active", "is_singleton": false, @@ -6516,11 +6516,11 @@ { "name": "ONT Sequencing Run", "polymorphic_discriminator": "data_template", - "category": "BDT", + "category": "BRN", "type": "sequencing_run", "subtype": "ont", "version": "1.0", - "instance_prefix": "BDT", + "instance_prefix": "BRN", "instance_polymorphic_identity": "data_instance", "bstatus": "active", "is_singleton": false, @@ -6552,13 +6552,13 @@ } }, { - "name": "NovaSeq Sequencing Run", + "name": "Ultima Sequencing Run", "polymorphic_discriminator": "data_template", - "category": "BDT", + "category": "BRT", "type": "sequencing_run", - "subtype": "novaseq", + "subtype": "ultima", "version": "1.0", - "instance_prefix": "BDT", + "instance_prefix": "BRT", "instance_polymorphic_identity": "data_instance", "bstatus": "active", "is_singleton": false, @@ -6569,20 +6569,96 @@ "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0", "set_object_status": "BAC/core/set_object_status/1.0" }, - "description": "Sequencing run executed on an Illumina NovaSeq instrument.", + "description": "Sequencing run executed on an Ultima instrument.", "expected_inputs": [], "expected_outputs": [], "instantiation_layouts": [], "properties": { "beta_kind": "sequencing_run", - "platform": "ILMN", - "run_subtype": "novaseq", + "platform": "Ultima", + "run_subtype": "ultima", + "flowcell_id": "", + "operator_start_datetime": null, + "sequencing_end_datetime": null, + "instrument_euid": "", + "metadata": {}, + "name": "Ultima Sequencing Run", + "idempotency_key": "" + }, + "singleton": "0", + "semantic_category": "data" + } + }, + { + "name": "CompleteGenomics Sequencing Run", + "polymorphic_discriminator": "data_template", + "category": "BRC", + "type": "sequencing_run", + "subtype": "completegenomics", + "version": "1.0", + "instance_prefix": "BRC", + "instance_polymorphic_identity": "data_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "action_groups": {}, + "action_imports": { + "add_relationships": "BAC/core/add-relationships/1.0", + "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0", + "set_object_status": "BAC/core/set_object_status/1.0" + }, + "description": "Sequencing run executed on a Complete Genomics instrument.", + "expected_inputs": [], + "expected_outputs": [], + "instantiation_layouts": [], + "properties": { + "beta_kind": "sequencing_run", + "platform": "CompleteGenomics", + "run_subtype": "completegenomics", + "flowcell_id": "", + "operator_start_datetime": null, + "sequencing_end_datetime": null, + "instrument_euid": "", + "metadata": {}, + "name": "CompleteGenomics Sequencing Run", + "idempotency_key": "" + }, + "singleton": "0", + "semantic_category": "data" + } + }, + { + "name": "PacBio Sequencing Run", + "polymorphic_discriminator": "data_template", + "category": "BRP", + "type": "sequencing_run", + "subtype": "pacbio", + "version": "1.0", + "instance_prefix": "BRP", + "instance_polymorphic_identity": "data_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "action_groups": {}, + "action_imports": { + "add_relationships": "BAC/core/add-relationships/1.0", + "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0", + "set_object_status": "BAC/core/set_object_status/1.0" + }, + "description": "Sequencing run executed on a PacBio instrument.", + "expected_inputs": [], + "expected_outputs": [], + "instantiation_layouts": [], + "properties": { + "beta_kind": "sequencing_run", + "platform": "PacBio", + "run_subtype": "pacbio", "flowcell_id": "", "operator_start_datetime": null, "sequencing_end_datetime": null, "instrument_euid": "", "metadata": {}, - "name": "NovaSeq Sequencing Run", + "name": "PacBio Sequencing Run", "idempotency_key": "" }, "singleton": "0", @@ -6630,7 +6706,7 @@ "relationship_type": "contains", "child_templates": [ { - "template_code": "BCN/shelf/generic/1.0", + "template_code": "BCR/shelf/generic/1.0", "json_addl": { "cont_address": { "capacity": "10", @@ -6643,7 +6719,7 @@ } }, { - "template_code": "BCN/shelf/generic/1.0", + "template_code": "BCR/shelf/generic/1.0", "json_addl": { "cont_address": { "capacity": "10", @@ -6712,7 +6788,7 @@ "relationship_type": "contains", "child_templates": [ { - "template_code": "BCN/shelf/generic/1.0", + "template_code": "BCR/shelf/generic/1.0", "json_addl": { "cont_address": { "capacity": "10", @@ -6725,7 +6801,7 @@ } }, { - "template_code": "BCN/shelf/generic/1.0", + "template_code": "BCR/shelf/generic/1.0", "json_addl": { "cont_address": { "capacity": "10", @@ -6738,7 +6814,7 @@ } }, { - "template_code": "BCN/shelf/generic/1.0", + "template_code": "BCR/shelf/generic/1.0", "json_addl": { "cont_address": { "capacity": "10", @@ -6751,7 +6827,7 @@ } }, { - "template_code": "BCN/shelf/generic/1.0", + "template_code": "BCR/shelf/generic/1.0", "json_addl": { "cont_address": { "capacity": "10", @@ -10382,6 +10458,3870 @@ }, "semantic_category": "workflow_step" } + }, + { + "name": "Sequencing Library Plate 96", + "polymorphic_discriminator": "container_template", + "category": "BCP", + "type": "plate", + "subtype": "sequencing-library-plate-96", + "version": "1.0", + "instance_prefix": "BCP", + "instance_polymorphic_identity": "container_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "action_groups": {}, + "action_imports": { + "add_relationships": "BAC/core/add-relationships/1.0", + "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0", + "download_plate_map": "BAC/plate/download_plate_map/1.0", + "print_barcode_label": "BAC/core/print_barcode_label/1.0", + "set_object_status": "BAC/core/set_object_status/1.0", + "stamp_plates_into_plate": "BAC/plate/stamp_plates_into_plate/1.0" + }, + "cogs": { + "allocation_type": "", + "cost": "4.00", + "cost_split_by_children": [ + { + "*/*/*/*": {} + } + ], + "state": "active" + }, + "cont_address": { + "col_idx": "0", + "col_name": "", + "row_idx": "0", + "row_name": "" + }, + "description": "96 well fixed plate", + "expected_inputs": [], + "expected_outputs": [], + "instantiation_layouts": [ + { + "relationship_type": "contains", + "child_templates": [ + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "0", + "col_name": "1", + "name": "A1", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A1" + } + }, + "name_pattern": "A1" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "1", + "col_name": "1", + "name": "A2", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A2" + } + }, + "name_pattern": "A2" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "2", + "col_name": "1", + "name": "A3", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A3" + } + }, + "name_pattern": "A3" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "3", + "col_name": "1", + "name": "A4", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A4" + } + }, + "name_pattern": "A4" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "4", + "col_name": "1", + "name": "A5", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A5" + } + }, + "name_pattern": "A5" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "5", + "col_name": "1", + "name": "A6", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A6" + } + }, + "name_pattern": "A6" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "6", + "col_name": "1", + "name": "A7", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A7" + } + }, + "name_pattern": "A7" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "7", + "col_name": "1", + "name": "A8", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A8" + } + }, + "name_pattern": "A8" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "8", + "col_name": "1", + "name": "A9", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A9" + } + }, + "name_pattern": "A9" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "9", + "col_name": "1", + "name": "A10", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A10" + } + }, + "name_pattern": "A10" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "10", + "col_name": "1", + "name": "A11", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A11" + } + }, + "name_pattern": "A11" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "11", + "col_name": "1", + "name": "A12", + "row_idx": "0", + "row_name": "A" + }, + "properties": { + "name": "A12" + } + }, + "name_pattern": "A12" + } + ] + }, + { + "relationship_type": "contains", + "child_templates": [ + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "0", + "col_name": "2", + "name": "B1", + "row_idx": "1", + "row_name": "B" + }, + "properties": { + "name": "B1" + } + }, + "name_pattern": "B1" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + "cont_address": { + "col_idx": "1", + "col_name": "2", + "name": "B2", + "row_idx": "1", + "row_name": "B" + }, + "properties": { + "name": "B2" + } + }, + "name_pattern": "B2" + }, + { + "template_code": "container/well/fixed-plate-well/*/", + "json_addl": { + 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Swab", + "instantiation_layouts": [], + "cogs": { + "state": "active", + "cost": "0.00", + "cost_split_by_children": [ + { + "*/*/*/*": {} + } + ], + "allocation_type": "" + }, + "properties": { + "name": "Saliva Specimen", + "volume": "", + "volume_units": "", + "comments": "", + "lab_code": "" + }, + "expected_inputs": [], + "singleton": "0", + "expected_outputs": [], + "actions": {}, + "semantic_category": "content" + } + }, + { + "name": "Sequencing Library Content", + "polymorphic_discriminator": "content_template", + "category": "BNQ", + "type": "sample", + "subtype": "sequencing-library", + "version": "1.0", + "instance_prefix": "BNQ", + "instance_polymorphic_identity": "content_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "description": "genomic DNA", + "properties": { + "name": "Sequencing Library Content", + "library_type": "", + "platform": "", + "volume": "", + "volume_units": "", + "comments": "", + "lab_code": "" + }, + "expected_inputs": [], + "singleton": "0", + "expected_outputs": [], + "actions": {}, + "instantiation_layouts": [], + "cogs": { + "state": "active", + "cost": "0.00", + "cost_split_by_children": [ + { + "*/*/*/*": {} + } + ], + "allocation_type": "" + }, + "semantic_category": "content" + } + }, + { + "name": "Sequencing Library Pool Content", + "polymorphic_discriminator": "content_template", + "category": "BNP", + "type": "pool", + "subtype": "sequencing-library", + "version": "1.0", + "instance_prefix": "BNP", + "instance_polymorphic_identity": "content_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "description": "Pool of Contents", + "properties": { + "name": "Sequencing Library Pool Content", + "platform": "", + "pool_strategy": "", + "member_count": 0, + "comments": "", + "lab_code": "" + }, + "expected_inputs": [], + "expected_outputs": [], + "singleton": "0", + "actions": {}, + "instantiation_layouts": [], + "cogs": { + "state": "active", + "cost": "0.00", + "cost_split_by_children": [ + { + "*/*/*/*": {} + } + ], + "allocation_type": "" + }, + "semantic_category": "content" + } + }, + { + "name": "Sequencing Index Reagent Content", + "polymorphic_discriminator": "content_template", + "category": "BNX", + "type": "reagent", + "subtype": "sequencing-index", + "version": "1.0", + "instance_prefix": "BNX", + "instance_polymorphic_identity": "content_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "description": "Novaseq sequencing kit", + "singleton": "0", + "properties": { + "name": "Sequencing Index Reagent Content", + "index_name": "", + "index_sequence": "", + "index_set": "", + "well_name": "", + "plate_euid": "", + "volume": "", + "volume_units": "", + "comments": "", + "manufacturer": "", + "lot_number": "", + "expiration_date": "", + "received_date": "", + "storage_conditions": "", + "qualification_status": "", + "lab_code": "" + }, + "expected_inputs": [], + "expected_outputs": [], + "actions": {}, + "instantiation_layouts": [], + "cogs": { + "state": "active", + "cost": "1.00", + "cost_split_by_children": [ + { + "*/*/*/*": {} + } + ], + "allocation_type": "" + }, + "semantic_category": "content" + } + }, + { + "name": "gDNA Quantification Data", + "polymorphic_discriminator": "data_template", + "category": "BDQ", + "type": "quantification", + "subtype": "gdna", + "version": "1.0", + "instance_prefix": "BDQ", + "instance_polymorphic_identity": "data_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "action_groups": {}, + "action_imports": { + "add_relationships": "BAC/core/add-relationships/1.0", + "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0", + "set_object_status": "BAC/core/set_object_status/1.0" + }, + "description": "Generic data record", + "expected_inputs": [], + "expected_outputs": [], + "instantiation_layouts": [], + "properties": { + "name": "gDNA Quantification Data", + "beta_kind": "gdna_quantification", + "target_euid": "", + "well_euid": "", + "well_name": "", + "method": "", + "concentration": null, + "concentration_units": "", + "total_yield": null, + "yield_units": "", + "passed": null, + "metadata": {}, + "idempotency_key": "" + }, + "singleton": "0", + "semantic_category": "data" + } + }, + { + "name": "Extraction Run Evidence", + "polymorphic_discriminator": "data_template", + "category": "BDX", + "type": "operation", + "subtype": "extraction", + "version": "1.0", + "instance_prefix": "BDX", + "instance_polymorphic_identity": "data_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "action_groups": {}, + "action_imports": { + "add_relationships": "BAC/core/add-relationships/1.0", + "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0", + "set_object_status": "BAC/core/set_object_status/1.0" + }, + "description": "Generic data record", + "expected_inputs": [], + "expected_outputs": [], + "instantiation_layouts": [], + "properties": { + "name": "Extraction Run Evidence", + "beta_kind": "extraction_run", + "operation_type": "extraction", + "source_specimen_euid": "", + "plate_euid": "", + "started_at": "", + "completed_at": "", + "reagent_euids": [], + "metadata": {}, + "idempotency_key": "" + }, + "singleton": "0", + "semantic_category": "data" + } + }, + { + "name": "Extraction QC Run Evidence", + "polymorphic_discriminator": "data_template", + "category": "BDY", + "type": "operation", + "subtype": "extraction-qc", + "version": "1.0", + "instance_prefix": "BDY", + "instance_polymorphic_identity": "data_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "action_groups": {}, + "action_imports": { + "add_relationships": "BAC/core/add-relationships/1.0", + "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0", + "set_object_status": "BAC/core/set_object_status/1.0" + }, + "description": "Generic data record", + "expected_inputs": [], + "expected_outputs": [], + "instantiation_layouts": [], + "properties": { + "name": "Extraction QC Run Evidence", + "beta_kind": "post_extract_qc_result", + "operation_type": "extraction_qc", + "extraction_output_euid": "", + "metrics": {}, + "passed": null, + "metadata": {}, + "idempotency_key": "" + }, + "singleton": "0", + "semantic_category": "data" + } + }, + { + "name": "Library Prep Run Evidence", + "polymorphic_discriminator": "data_template", + "category": "BDP", + "type": "operation", + "subtype": "library-prep", + "version": "1.0", + "instance_prefix": "BDP", + "instance_polymorphic_identity": "data_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "action_groups": {}, + "action_imports": { + "add_relationships": "BAC/core/add-relationships/1.0", + "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0", + "set_object_status": "BAC/core/set_object_status/1.0" + }, + "description": "Generic data record", + "expected_inputs": [], + "expected_outputs": [], + "instantiation_layouts": [], + "properties": { + "name": "Library Prep Run Evidence", + "beta_kind": "library_prep_output", + "operation_type": "library_prep", + "platform": "", + "source_extraction_output_euid": "", + "reagent_euids": [], + "metadata": {}, + "idempotency_key": "" + }, + "singleton": "0", + "semantic_category": "data" + } + }, + { + "name": "Pooling Run Evidence", + "polymorphic_discriminator": "data_template", + "category": "BDN", + "type": "operation", + "subtype": "pooling", + "version": "1.0", + "instance_prefix": "BDN", + "instance_polymorphic_identity": "data_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "action_groups": {}, + "action_imports": { + "add_relationships": "BAC/core/add-relationships/1.0", + "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0", + "set_object_status": "BAC/core/set_object_status/1.0" + }, + "description": "Generic data record", + "expected_inputs": [], + "expected_outputs": [], + "instantiation_layouts": [], + "properties": { + "name": "Pooling Run Evidence", + "beta_kind": "pooling_run", + "operation_type": "pooling", + "platform": "", + "member_euids": [], + "pool_euid": "", + "metadata": {}, + "idempotency_key": "" + }, + "singleton": "0", + "semantic_category": "data" + } + }, + { + "name": "Library Index Assignment Data", + "polymorphic_discriminator": "data_template", + "category": "BDA", + "type": "library-index-assignment", + "subtype": "sequencing-library", + "version": "1.0", + "instance_prefix": "BDA", + "instance_polymorphic_identity": "data_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "action_groups": {}, + "action_imports": { + "add_relationships": "BAC/core/add-relationships/1.0", + "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0", + "set_object_status": "BAC/core/set_object_status/1.0" + }, + "description": "Generic data record", + "expected_inputs": [], + "expected_outputs": [], + "instantiation_layouts": [], + "properties": { + "name": "Library Index Assignment Data", + "beta_kind": "sequenced_library_assignment", + "flowcell_id": "", + "lane": "", + "library_barcode": "", + "library_prep_output_euid": "", + "library_material_euid": "", + "barcode_reagent_euid": "", + "metadata": {}, + "idempotency_key": "" + }, + "singleton": "0", + "semantic_category": "data" + } + }, + { + "name": "Transfer Execution Data", + "polymorphic_discriminator": "data_template", + "category": "BDT", + "type": "execution", + "subtype": "transfer", + "version": "1.0", + "instance_prefix": "BDT", + "instance_polymorphic_identity": "data_instance", + "bstatus": "active", + "is_singleton": false, + "json_addl": { + "action_groups": {}, + "action_imports": { + "add_relationships": "BAC/core/add-relationships/1.0", + "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0", + "set_object_status": "BAC/core/set_object_status/1.0" + }, + "description": "Generic data record", + "expected_inputs": [], + "expected_outputs": [], + "instantiation_layouts": [], + "properties": { + "name": "Transfer Execution Data", + "beta_kind": "transfer_execution", + "source_euid": "", + "destination_euid": "", + "transfer_type": "", + "status": "", + "metadata": {}, + "idempotency_key": "" + }, + "singleton": "0", + "semantic_category": "data" + } } ] } diff --git a/tests/test_bloom_prefix_taxonomy.py b/tests/test_bloom_prefix_taxonomy.py new file mode 100644 index 0000000..119c60a --- /dev/null +++ b/tests/test_bloom_prefix_taxonomy.py @@ -0,0 +1,162 @@ +"""Bloom prefix taxonomy and wet-lab template contract tests.""" + +from __future__ import annotations + +import json +from pathlib import Path + +import pytest + +from bloom_lims.core.validation import ValidationError, validate_euid + + +PROJECT_ROOT = Path(__file__).resolve().parents[1] +FORBIDDEN_PREFIX_CHARS = set("ILOU") + + +def _template_pack() -> dict: + return json.loads( + ( + PROJECT_ROOT / "config" / "tapdb_templates" / "bloom" / "templates.json" + ).read_text(encoding="utf-8") + ) + + +def _templates_by_code() -> dict[str, dict]: + templates: dict[str, dict] = {} + for template in _template_pack()["templates"]: + semantic_category = template["json_addl"].get("semantic_category") + code = ( + f"{semantic_category}/{template['type']}/" + f"{template['subtype']}/{template['version']}" + ) + templates[code] = template + return templates + + +def test_wet_lab_templates_use_bloom_prefix_taxonomy() -> None: + templates = _templates_by_code() + + expected_prefixes = { + "container/tube/tube-generic-10ml/1.0": "BCT", + "container/plate/fixed-plate-96/1.0": "BCP", + "container/plate/sequencing-library-plate-96/1.0": "BCP", + "container/plate/index-plate-96/1.0": "BCP", + "container/well/fixed-plate-well/1.0": "BCW", + "container/bottle/generic/1.0": "BCB", + "container/flowcell/generic/1.0": "BCF", + "container/flowcell_lane/generic/1.0": "BCE", + "content/specimen/blood-whole/1.0": "BNB", + "content/specimen/buccal-swab/1.0": "BNS", + "content/specimen/saliva/1.0": "BNA", + "content/sample/gdna/1.0": "BNG", + "content/sample/cfdna/1.0": "BNC", + "content/sample/sequencing-library/1.0": "BNQ", + "content/pool/sequencing-library/1.0": "BNP", + "content/reagent/sequencing-index/1.0": "BNX", + "data/generic/gdna-quantification/1.0": "BDQ", + "data/quantification/gdna/1.0": "BDQ", + "data/operation/extraction/1.0": "BDX", + "data/operation/extraction-qc/1.0": "BDY", + "data/operation/library-prep/1.0": "BDP", + "data/operation/pooling/1.0": "BDN", + "data/library-index-assignment/sequencing-library/1.0": "BDA", + "data/execution/transfer/1.0": "BDT", + "generic/generic/external_object_link/1.0": "BGX", + } + + for code, expected_prefix in expected_prefixes.items(): + template = templates[code] + assert template["category"] == expected_prefix + assert template["instance_prefix"] == expected_prefix + + +def test_prefix_taxonomy_rejects_forbidden_letters_and_leading_zero_examples() -> None: + prefixes = { + template["instance_prefix"] + for template in _template_pack()["templates"] + if template.get("instance_prefix") + } + registry = json.loads( + ( + PROJECT_ROOT / "bloom_lims" / "etc" / "prefix_ownership_registry.json" + ).read_text(encoding="utf-8") + ) + prefixes.update(registry["ownership"]["Z"]) + + assert all(not (set(prefix) & FORBIDDEN_PREFIX_CHARS) for prefix in prefixes) + for bad_prefix in ("BCL", "BRI", "BRO", "BRU", "BNL", "BDL"): + assert bad_prefix not in prefixes + + assert validate_euid("BCP1") + assert validate_euid("BD1") + with pytest.raises(ValidationError, match="No leading zeros"): + validate_euid("BCP01") + + +def test_prefixes_are_declared_in_packaged_ownership_registry() -> None: + registry = json.loads( + ( + PROJECT_ROOT / "bloom_lims" / "etc" / "prefix_ownership_registry.json" + ).read_text(encoding="utf-8") + ) + claims = registry["ownership"]["Z"] + + for prefix in { + "BC", + "BCT", + "BCP", + "BCW", + "BCB", + "BCF", + "BCE", + "BCR", + "BN", + "BNB", + "BNS", + "BNA", + "BNG", + "BNC", + "BNQ", + "BNP", + "BNR", + "BNX", + "BNK", + "BD", + "BDQ", + "BDX", + "BDY", + "BDP", + "BDN", + "BDA", + "BDT", + "BR", + "BRM", + "BRN", + "BRT", + "BRP", + "BRC", + "BG", + "BGX", + "BGM", + "BGP", + "BGV", + "BGR", + "BGS", + }: + assert claims[prefix]["issuer_app_code"] == "bloom" + + +def test_readme_documents_taxonomy_and_historical_object_rule() -> None: + readme = (PROJECT_ROOT / "README.md").read_text(encoding="utf-8") + + for snippet in ( + "BC*` | Containers", + "BN*` | Contents, materials, and reagents", + "BD*` | Data and evidence objects", + "BR*` | Runs and executions", + "BG*` | Generic helpers and external-object mappings", + "Existing historical objects keep their already minted EUIDs", + "Prefixes are governance and display labels only", + ): + assert snippet in readme diff --git a/tests/test_queue_flow.py b/tests/test_queue_flow.py index 071959f..c5e508b 100644 --- a/tests/test_queue_flow.py +++ b/tests/test_queue_flow.py @@ -249,8 +249,8 @@ def test_beta_queue_flow_end_to_end(): extraction_body["atlas_test_fulfillment_item_euid"] == atlas_context["fulfillment_items"][0]["atlas_test_fulfillment_item_euid"] ) - _assert_domain_scoped_euid(extraction_body["extraction_batch_euid"], "BDT-") - _assert_domain_scoped_euid(extraction_body["extraction_run_euid"], "BDT-") + _assert_domain_scoped_euid(extraction_body["extraction_batch_euid"], "BDX-") + _assert_domain_scoped_euid(extraction_body["extraction_run_euid"], "BDX-") extraction_output_euid = extraction_body["extraction_output_euid"] extraction_batch_euid = extraction_body["extraction_batch_euid"] extraction_run_euid = extraction_body["extraction_run_euid"] @@ -281,7 +281,7 @@ def test_beta_queue_flow_end_to_end(): qc_body = qc.json() assert qc_body["current_queue"] == "ilmn_lib_prep" assert qc_body["next_queue"] == "ilmn_lib_prep" - _assert_domain_scoped_euid(qc_body["qc_record_euid"], "BDT-") + _assert_domain_scoped_euid(qc_body["qc_record_euid"], "BDY-") ont_library_prep = client.post( "/api/v1/external/atlas/beta/library-prep", @@ -316,10 +316,10 @@ def test_beta_queue_flow_end_to_end(): library_container_euid = library_body["library_container_euid"] library_plate_euid = library_body["library_plate_euid"] library_well_euid = library_body["library_well_euid"] - _assert_domain_scoped_euid(library_material_euid, "BCT-") - _assert_domain_scoped_euid(library_container_euid, "BCN-") - _assert_domain_scoped_euid(library_plate_euid, "BCN-") - _assert_domain_scoped_euid(library_well_euid, "BCN-") + _assert_domain_scoped_euid(library_material_euid, "BNQ-") + _assert_domain_scoped_euid(library_container_euid, "BCP-") + _assert_domain_scoped_euid(library_plate_euid, "BCP-") + _assert_domain_scoped_euid(library_well_euid, "BCW-") library_qc = client.post( "/api/v1/external/atlas/beta/library-qc", @@ -337,7 +337,7 @@ def test_beta_queue_flow_end_to_end(): assert library_qc_body["qc_passed"] is True assert library_qc_body["next_queue"] == "ilmn_seq_pool" assert library_qc_body["current_queue"] == "ilmn_seq_pool" - _assert_domain_scoped_euid(library_qc_body["qc_record_euid"], "BDT-") + _assert_domain_scoped_euid(library_qc_body["qc_record_euid"], "BDP-") pool = client.post( "/api/v1/external/atlas/beta/pools", @@ -367,7 +367,7 @@ def test_beta_queue_flow_end_to_end(): json={ "pool_euid": pool_euid, "platform": "ILMN", - "run_subtype": "novaseq", + "run_subtype": "illumina", "flowcell_id": flowcell_id, "run_name": "beta-ilmn-run", "status": "completed", @@ -402,7 +402,7 @@ def test_beta_queue_flow_end_to_end(): assert run_body["artifact_count"] == 1 assert run_body["assignment_count"] == 1 assert run_body["flowcell_id"] == flowcell_id - assert run_body["run_subtype"] == "novaseq" + assert run_body["run_subtype"] == "illumina" assert run_body["operator_start_datetime"] == "2026-05-20T06:00:00Z" assert run_body["sequencing_end_datetime"] == "2026-05-20T14:30:00Z" assert run_body["instrument_euid"] == instrument_euid @@ -421,9 +421,9 @@ def test_beta_queue_flow_end_to_end(): ) run_props = (run_instance.json_addl or {}).get("properties", {}) assert run_instance.type == "sequencing_run" - assert run_instance.subtype == "novaseq" + assert run_instance.subtype == "illumina" assert run_props["beta_kind"] == "sequencing_run" - assert run_props["run_subtype"] == "novaseq" + assert run_props["run_subtype"] == "illumina" assert run_props["operator_start_datetime"] == "2026-05-20T06:00:00+00:00" assert run_props["sequencing_end_datetime"] == "2026-05-20T14:30:00+00:00" assert run_props["instrument_euid"] == instrument_euid diff --git a/tests/test_sequencing_run_contract.py b/tests/test_sequencing_run_contract.py index 14c04b4..cb6d1c2 100644 --- a/tests/test_sequencing_run_contract.py +++ b/tests/test_sequencing_run_contract.py @@ -16,7 +16,7 @@ def _minimal_run_payload(**overrides): payload = { - "pool_euid": "BCT-POOL-1", + "pool_euid": "BNP-POOL-1", "platform": "ILMN", "run_subtype": "illumina", "flowcell_id": "FLOW-1", @@ -26,7 +26,7 @@ def _minimal_run_payload(**overrides): { "lane": "1", "library_barcode": "IDX-1", - "library_prep_output_euid": "BDT-LIB-1", + "library_prep_output_euid": "BDP-LIB-1", } ], } @@ -51,15 +51,21 @@ def test_sequencing_run_templates_are_shipped_for_tapdb_seed(): } expected = { - ("data", "sequencing_run", "illumina", "1.0"): "ILMN", - ("data", "sequencing_run", "ont", "1.0"): "ONT", - ("data", "sequencing_run", "novaseq", "1.0"): "ILMN", + ("data", "sequencing_run", "illumina", "1.0"): ("ILMN", "BRM"), + ("data", "sequencing_run", "ont", "1.0"): ("ONT", "BRN"), + ("data", "sequencing_run", "ultima", "1.0"): ("Ultima", "BRT"), + ("data", "sequencing_run", "completegenomics", "1.0"): ( + "CompleteGenomics", + "BRC", + ), + ("data", "sequencing_run", "pacbio", "1.0"): ("PacBio", "BRP"), } - for template_key, platform in expected.items(): + for template_key, (platform, instance_prefix) in expected.items(): template = templates[template_key] props = template["json_addl"]["properties"] - assert template["category"] == "BDT" - assert template["instance_prefix"] == "BDT" + assert template["category"] == instance_prefix + assert template["instance_prefix"] == instance_prefix + assert template["json_addl"]["semantic_category"] == "data" assert props["beta_kind"] == "sequencing_run" assert props["platform"] == platform assert props["run_subtype"] == template_key[2] @@ -69,18 +75,24 @@ def test_sequencing_run_templates_are_shipped_for_tapdb_seed(): def test_run_schema_validates_subtype_platform_and_datetime_contract(): - novaseq = BetaRunCreateRequest.model_validate( - _minimal_run_payload(run_subtype="novaseq") - ) - assert novaseq.run_subtype == "novaseq" - - ont = BetaRunCreateRequest.model_validate( - _minimal_run_payload(platform="ONT", run_subtype="ont") - ) - assert ont.platform == "ONT" + expected = { + "ILMN": "illumina", + "ONT": "ont", + "Ultima": "ultima", + "PacBio": "pacbio", + "CompleteGenomics": "completegenomics", + } + for platform, run_subtype in expected.items(): + run = BetaRunCreateRequest.model_validate( + _minimal_run_payload(platform=platform, run_subtype=run_subtype) + ) + assert run.platform == platform + assert run.run_subtype == run_subtype with pytest.raises(ValidationError, match="platform=ONT requires run_subtype=ont"): - BetaRunCreateRequest.model_validate(_minimal_run_payload(platform="ONT")) + BetaRunCreateRequest.model_validate( + _minimal_run_payload(platform="ONT", run_subtype="illumina") + ) with pytest.raises(ValidationError, match="must include a timezone"): BetaRunCreateRequest.model_validate( From 3bfa5b5f7f4078cf25d92b12fbfbd29e31c27dcf Mon Sep 17 00:00:00 2001 From: John Major Date: Tue, 2 Jun 2026 00:43:03 -0700 Subject: [PATCH 08/47] Repair Bloom EUID actions and retire queue GUI --- bloom_lims/config/action/core.json | 58 +++++++++++++++++++-- bloom_lims/gui/actions.py | 39 +++++++++++++- bloom_lims/gui/routes/operations.py | 23 ++++++-- templates/modern/base.html | 3 -- templates/modern/dashboard.html | 42 --------------- templates/modern/euid_details.html | 44 +++++++--------- templates/modern/queue_retired.html | 28 ++++++++++ tests/test_action_button_template_safety.py | 7 +++ tests/test_action_schema_hydration.py | 54 +++++++++++++++++++ tests/test_gui_endpoints.py | 17 +++--- 10 files changed, 229 insertions(+), 86 deletions(-) create mode 100644 templates/modern/queue_retired.html diff --git a/bloom_lims/config/action/core.json b/bloom_lims/config/action/core.json index 5951321..dff7c65 100644 --- a/bloom_lims/config/action/core.json +++ b/bloom_lims/config/action/core.json @@ -47,7 +47,7 @@ "label_style": "" }, "curr_user": "", - "description": "Print Label2", + "description": "Print Label", "ui_schema": { "title": "Print Label", "fields": [] @@ -78,7 +78,58 @@ "description": "Add Parent or Child Relationships (aka lineages).", "ui_schema": { "title": "Add Parent or Child Relationship(s)", - "fields": [] + "fields": [ + { + "name": "lineage_type_to_create", + "label": "Create Relationship As", + "type": "select", + "required": true, + "options": [ + {"value": "parent", "label": "parent"}, + {"value": "child", "label": "child"} + ] + }, + { + "name": "relationship_type", + "label": "Relationship Type", + "type": "select", + "required": true, + "options": [ + {"value": "contains", "label": "contains"}, + {"value": "derived_from", "label": "derived_from"}, + {"value": "aliquot_of", "label": "aliquot_of"}, + {"value": "prepared_from", "label": "prepared_from"}, + {"value": "member_of", "label": "member_of"}, + {"value": "has_external_reference", "label": "has_external_reference"}, + {"value": "beta_extraction_batch_run", "label": "beta_extraction_batch_run"}, + {"value": "beta_extraction_run_input", "label": "beta_extraction_run_input"}, + {"value": "beta_extraction_plate", "label": "beta_extraction_plate"}, + {"value": "beta_extraction_well", "label": "beta_extraction_well"}, + {"value": "beta_extraction_output", "label": "beta_extraction_output"}, + {"value": "beta_extraction_run_output", "label": "beta_extraction_run_output"}, + {"value": "beta_post_extract_qc", "label": "beta_post_extract_qc"}, + {"value": "beta_library_prep_output", "label": "beta_library_prep_output"}, + {"value": "beta_library_material_output", "label": "beta_library_material_output"}, + {"value": "beta_library_qc", "label": "beta_library_qc"}, + {"value": "beta_pooling_run_output", "label": "beta_pooling_run_output"}, + {"value": "beta_pool_member", "label": "beta_pool_member"}, + {"value": "beta_pooling_run_input", "label": "beta_pooling_run_input"}, + {"value": "beta_sequencing_run", "label": "beta_sequencing_run"}, + {"value": "beta_sequenced_library_assignment", "label": "beta_sequenced_library_assignment"}, + {"value": "beta_assignment_source", "label": "beta_assignment_source"}, + {"value": "beta_assignment_library_material", "label": "beta_assignment_library_material"}, + {"value": "beta_assignment_barcode_reagent", "label": "beta_assignment_barcode_reagent"}, + {"value": "beta_run_artifact", "label": "beta_run_artifact"} + ] + }, + { + "name": "euids", + "label": "EUIDs (one per line)", + "type": "textarea", + "required": true, + "rows": 6 + } + ] } } } @@ -90,7 +141,8 @@ "method_name": "do_action_create_subject_and_anchor", "action_executed": "0", "max_executions": "-1", - "action_enabled": "1", + "action_enabled": "0", + "action_visible": "0", "capture_data": "yes", "captured_data": {}, "deactivate_actions_when_executed": [], diff --git a/bloom_lims/gui/actions.py b/bloom_lims/gui/actions.py index 32d7cdb..a41d394 100644 --- a/bloom_lims/gui/actions.py +++ b/bloom_lims/gui/actions.py @@ -4,6 +4,34 @@ from bloom_lims.domain import BloomObj +RELATIONSHIP_TYPE_OPTIONS = [ + {"value": "contains", "label": "contains"}, + {"value": "derived_from", "label": "derived_from"}, + {"value": "aliquot_of", "label": "aliquot_of"}, + {"value": "prepared_from", "label": "prepared_from"}, + {"value": "member_of", "label": "member_of"}, + {"value": "has_external_reference", "label": "has_external_reference"}, + {"value": "beta_extraction_batch_run", "label": "beta_extraction_batch_run"}, + {"value": "beta_extraction_run_input", "label": "beta_extraction_run_input"}, + {"value": "beta_extraction_plate", "label": "beta_extraction_plate"}, + {"value": "beta_extraction_well", "label": "beta_extraction_well"}, + {"value": "beta_extraction_output", "label": "beta_extraction_output"}, + {"value": "beta_extraction_run_output", "label": "beta_extraction_run_output"}, + {"value": "beta_post_extract_qc", "label": "beta_post_extract_qc"}, + {"value": "beta_library_prep_output", "label": "beta_library_prep_output"}, + {"value": "beta_library_material_output", "label": "beta_library_material_output"}, + {"value": "beta_library_qc", "label": "beta_library_qc"}, + {"value": "beta_pooling_run_output", "label": "beta_pooling_run_output"}, + {"value": "beta_pool_member", "label": "beta_pool_member"}, + {"value": "beta_pooling_run_input", "label": "beta_pooling_run_input"}, + {"value": "beta_sequencing_run", "label": "beta_sequencing_run"}, + {"value": "beta_sequenced_library_assignment", "label": "beta_sequenced_library_assignment"}, + {"value": "beta_assignment_source", "label": "beta_assignment_source"}, + {"value": "beta_assignment_library_material", "label": "beta_assignment_library_material"}, + {"value": "beta_assignment_barcode_reagent", "label": "beta_assignment_barcode_reagent"}, + {"value": "beta_run_artifact", "label": "beta_run_artifact"}, +] + def _normalize_action_slug(action_data: dict) -> str: method_name = str(action_data.get("method_name") or "").strip() @@ -46,8 +74,9 @@ def _default_ui_fields_for_action(action_data: dict) -> list[dict]: { "name": "relationship_type", "label": "Relationship Type", - "type": "text", + "type": "select", "required": True, + "options": RELATIONSHIP_TYPE_OPTIONS, }, { "name": "euids", @@ -74,9 +103,15 @@ def hydrate_dynamic_action_groups(action_groups: dict, bobdb: BloomObj) -> dict: actions = group_data.get("actions", {}) if not isinstance(actions, dict): continue - for action_data in actions.values(): + for action_key, action_data in list(actions.items()): if not isinstance(action_data, dict): continue + if ( + action_data.get("action_visible") == "0" + or _normalize_action_slug(action_data) == "create_subject_and_anchor" + ): + actions.pop(action_key, None) + continue captured = action_data.get("captured_data") if not isinstance(captured, dict): captured = {} diff --git a/bloom_lims/gui/routes/operations.py b/bloom_lims/gui/routes/operations.py index 518e540..550124b 100644 --- a/bloom_lims/gui/routes/operations.py +++ b/bloom_lims/gui/routes/operations.py @@ -547,13 +547,30 @@ async def update_preference(request: Request, auth: dict = Depends(require_auth) @router.get("/queue_details", response_class=HTMLResponse) async def queue_details( - request: Request, queue_euid, page=1, _auth=Depends(require_auth) + request: Request, + queue_euid: str | None = Query(default=None), + euid: str | None = Query(default=None), + page=1, + _auth=Depends(require_auth), ): + queue_euid = str(queue_euid or euid or "").strip() + user_data = request.session.get("user_data", {}) + if not queue_euid: + template = templates.get_template("modern/queue_retired.html") + return HTMLResponse( + content=template.render( + { + "request": request, + "udat": user_data, + "queue_euid": "", + } + ) + ) + page = int(page) if page < 1: page = 1 per_page = 500 - user_logged_in = True if "user_data" in request.session else False bobdb = BloomObj(BLOOMdb3(app_username=request.session["user_data"]["email"])) queue = bobdb.get_by_euid(queue_euid) qm = [] @@ -563,8 +580,6 @@ async def queue_details( queue_details = queue.sort_by_euid(qm) queue_details_list = queue_details[(page - 1) * per_page : page * per_page] pagination = {"next": page + 1, "prev": page - 1, "euid": queue_euid} - user_data = request.session.get("user_data", {}) - queue.items = queue_details_list template = templates.get_template("modern/queue_details.html") diff --git a/templates/modern/base.html b/templates/modern/base.html index f85249d..ecdb0da 100644 --- a/templates/modern/base.html +++ b/templates/modern/base.html @@ -63,9 +63,6 @@ Dashboard - - Queue Runtime - Equipment diff --git a/templates/modern/dashboard.html b/templates/modern/dashboard.html index 27ee403..dd56dc1 100644 --- a/templates/modern/dashboard.html +++ b/templates/modern/dashboard.html @@ -17,16 +17,6 @@

Dashboard

- -
- -
-
-
{{ stats.queue_runtime_total | default(0) }}
-
Queue Runtime Objects
-
- -
@@ -60,37 +50,6 @@

Dashboard

- -
-
-

Recent Queue Runtime

- View All -
-
- {% if recent_queue_runtime %} -
- {% for queue_item in recent_queue_runtime[:5] %} - -
- {{ queue_item.euid }} - {{ queue_item.name | default(queue_item.euid) }} -
- - {{ queue_item.status | default('active') }} - - - {% endfor %} -
- {% else %} -
-
-

No recent queue runtime objects

- Open Queue Runtime -
- {% endif %} -
-
-
@@ -129,7 +88,6 @@

Quick Actions

- Queue Runtime Equipment Reagents Templates diff --git a/templates/modern/euid_details.html b/templates/modern/euid_details.html index 2bcbaa0..56ec80f 100644 --- a/templates/modern/euid_details.html +++ b/templates/modern/euid_details.html @@ -160,9 +160,6 @@

Actions

Related Objects -
@@ -779,23 +776,27 @@

Full JSON (json_addl)

var editorProperties = null; var editorTemplate = null; -// Collapsible section toggle -document.querySelectorAll('.collapsible-btn').forEach(function(btn) { - btn.addEventListener('click', function() { - var targetId = this.getAttribute('data-target'); - var targetEl = document.getElementById(targetId); - - // Toggle active class on button - this.classList.toggle('active'); - - // Toggle visibility of content - if (targetEl.style.display === 'none') { - targetEl.style.display = 'block'; - } else { - targetEl.style.display = 'none'; - } +function bindCollapsibleSections() { + document.querySelectorAll('.collapsible-btn').forEach(function(btn) { + if (btn.dataset.bound === '1') return; + btn.dataset.bound = '1'; + btn.addEventListener('click', function() { + var targetId = this.getAttribute('data-target'); + var targetEl = document.getElementById(targetId); + if (!targetEl) { + if (typeof window.BloomToast !== 'undefined' && typeof window.BloomToast.error === 'function') { + window.BloomToast.error('Section Missing', 'Unable to find section ' + targetId); + } + return; + } + this.classList.toggle('active'); + targetEl.style.display = targetEl.style.display === 'none' || targetEl.style.display === '' ? 'block' : 'none'; + }); }); -}); +} + +bindCollapsibleSections(); +document.addEventListener('DOMContentLoaded', bindCollapsibleSections); // Format JSON on page load document.addEventListener('DOMContentLoaded', function() { @@ -957,11 +958,6 @@

Full JSON (json_addl)

} } -// Print label -function printLabel(euid) { - BloomToast.info('Print Label', 'Printing label for ' + euid); -} - // Edit mode state var isEditMode = false; var editorFull = null; diff --git a/templates/modern/queue_retired.html b/templates/modern/queue_retired.html new file mode 100644 index 0000000..316fa67 --- /dev/null +++ b/templates/modern/queue_retired.html @@ -0,0 +1,28 @@ +{% extends "modern/base.html" %} + +{% block title %}Queue Runtime Retired - BLOOM LIMS{% endblock %} + +{% block content %} +
+

Queue Runtime Hidden

+

+ Bloom queue runtime pages are retired from the production GUI while queue execution moves to the dedicated workflow service. +

+
+ +
+
+

Queue GUI Retired

+
+
+

+ Existing queue records are unchanged, but the Bloom dashboard no longer exposes queue runtime navigation. + Use object search or EUID details for retained Bloom objects. +

+
+ Dashboard + Search Objects +
+
+
+{% endblock %} diff --git a/tests/test_action_button_template_safety.py b/tests/test_action_button_template_safety.py index be00720..b06b0a8 100644 --- a/tests/test_action_button_template_safety.py +++ b/tests/test_action_button_template_safety.py @@ -18,6 +18,13 @@ def test_modern_euid_details_uses_data_attribute_action_handler(): assert "onclick=\"showCapturedDataForm(this, {{ action_value | tojson }}" not in template +def test_modern_euid_details_has_no_toast_only_print_button(): + template = _read("templates/modern/euid_details.html") + + assert "onclick=\"printLabel('{{ obj.euid }}')\"" not in template + assert "Printing label for " not in template + + def test_modern_workflow_details_uses_data_attribute_action_handler(): template = _read("templates/modern/workflow_details.html") diff --git a/tests/test_action_schema_hydration.py b/tests/test_action_schema_hydration.py index 2b65717..2b508d1 100644 --- a/tests/test_action_schema_hydration.py +++ b/tests/test_action_schema_hydration.py @@ -44,3 +44,57 @@ def test_hydrate_dynamic_action_groups_removes_retired_assay_markup(): assert original_action["captured_data"] == {} assert "___workflow/assay/" not in hydrated_action["captured_data"] assert hydrated_action["ui_schema"]["fields"] == [] + + +def test_hydrate_dynamic_action_groups_adds_relationship_type_dropdown(): + action_groups = { + "core": { + "group_name": "Core Actions", + "actions": { + "action/core/add-relationships/1.0": { + "method_name": "do_action_add_relationships", + "capture_data": "yes", + "captured_data": {}, + "ui_schema": {"title": "Add Relationships", "fields": []}, + } + }, + } + } + + hydrated = hydrate_dynamic_action_groups(action_groups, SimpleNamespace()) + fields = hydrated["core"]["actions"]["action/core/add-relationships/1.0"][ + "ui_schema" + ]["fields"] + relationship_field = next( + field for field in fields if field["name"] == "relationship_type" + ) + + assert relationship_field["type"] == "select" + assert relationship_field["required"] is True + assert {"value": "derived_from", "label": "derived_from"} in relationship_field[ + "options" + ] + assert {"value": "beta_sequencing_run", "label": "beta_sequencing_run"} in relationship_field[ + "options" + ] + + +def test_hydrate_dynamic_action_groups_hides_subject_decision_scope_action(): + action_groups = { + "core": { + "group_name": "Core Actions", + "actions": { + "action/core/create-subject-and-anchor/1.0": { + "method_name": "do_action_create_subject_and_anchor", + "action_visible": "0", + "capture_data": "yes", + "captured_data": {}, + "ui_schema": {"title": "Create Subject", "fields": []}, + } + }, + } + } + + hydrated = hydrate_dynamic_action_groups(action_groups, SimpleNamespace()) + + assert hydrated["core"]["actions"] == {} diff --git a/tests/test_gui_endpoints.py b/tests/test_gui_endpoints.py index a290ad0..f7a117c 100644 --- a/tests/test_gui_endpoints.py +++ b/tests/test_gui_endpoints.py @@ -451,11 +451,11 @@ class TestQueueEndpoints: """Tests for queue management endpoints.""" def test_queue_details_returns_html(self, client): - """Test queue details returns HTML.""" + """Bare queue details route renders the retired queue GUI explanation.""" response = client.get("/queue_details") - assert response.status_code in [200, 422, 500] - if response.status_code == 200: - assert "text/html" in response.headers["content-type"] + assert response.status_code == 200 + assert "text/html" in response.headers["content-type"] + assert "Queue Runtime Hidden" in response.text def test_set_filter(self, client): """Test set filter endpoint works.""" @@ -653,11 +653,11 @@ def test_footer_has_version(self, client): assert "footer" in content.lower() def test_pages_have_breadcrumb_or_header(self, client): - """Queue runtime remains visible from the dashboard after assay-page retirement.""" + """Dashboard renders normal modern page header after queue GUI retirement.""" response = client.get("/") assert response.status_code == 200 content = response.text - assert "page-header" in content or "Queue Runtime" in content + assert "page-header" in content class TestModernAPIs: @@ -960,7 +960,7 @@ def test_dashboard_has_navigation_links(self, client): # Check for main navigation links assert 'href="/"' in content # Dashboard - assert 'href="/queue_details"' in content + assert 'href="/queue_details"' not in content assert 'href="/assays"' not in content assert 'href="/workflows"' not in content assert 'href="/admin"' in content @@ -1789,7 +1789,8 @@ class TestQueueEndpointsV2: def test_queue_details_no_params(self, client): """Test queue details without parameters.""" response = client.get("/queue_details") - assert response.status_code in [200, 302, 307, 400, 422, 500] + assert response.status_code == 200 + assert "Queue Runtime Hidden" in response.text def test_queue_details_with_euid(self, client): """Test queue details with EUID.""" From a2b6d5706b9878648db60d9e8ce0b0fd5beeda27 Mon Sep 17 00:00:00 2001 From: John Major Date: Thu, 4 Jun 2026 13:35:17 -0700 Subject: [PATCH 09/47] Release Bloom 6.0.0 TapDB UI updates --- ...604T110700Z_access_logging_ai_agent_gap.md | 24 +++++ pyproject.toml | 2 +- static/js/graph.js | 42 +++++++-- static/modern/css/bloom_modern.css | 93 +++++++++++++++++++ static/modern/js/lsmc_ui.js | 74 +++++++++++++++ templates/modern/base.html | 3 +- templates/modern/dag_explorer.html | 11 ++- tests/test_cytoscape_dag.py | 12 +++ uv.lock | 16 ++-- 9 files changed, 258 insertions(+), 19 deletions(-) create mode 100644 docs/plans/20260604T110700Z_access_logging_ai_agent_gap.md create mode 100644 static/modern/js/lsmc_ui.js diff --git a/docs/plans/20260604T110700Z_access_logging_ai_agent_gap.md b/docs/plans/20260604T110700Z_access_logging_ai_agent_gap.md new file mode 100644 index 0000000..147eee8 --- /dev/null +++ b/docs/plans/20260604T110700Z_access_logging_ai_agent_gap.md @@ -0,0 +1,24 @@ +# Bloom Access Logging And AI-Agent Read Access Gap + +Created: 2026-06-04T11:07:00Z + +## Status + +Bloom needs a follow-up implementation pass before Kahlo-issued AI-agent tokens can safely read Bloom search endpoints directly. + +## Required Contract + +- Validate Kahlo-issued AI-agent bearer tokens against an explicit Dayhoff-generated allowlist. +- Accept only read-only endpoint IDs approved for Bloom search/detail APIs. +- Record every endpoint access with request ID, correlation ID, route template, status, duration, client IP, auth mode, human user, service ID, AI-agent ID, authorizing human, token ID prefix/hash, scopes, and denial reason. +- Never log bearer tokens, cookies, raw presigned URLs, PHI-bearing query strings, object keys, or raw request/response bodies. + +## Current Gap + +Current source does not prove uniform all-endpoint structured access logs with actor/IP/AI-agent provenance, and it does not validate Kahlo-issued AI-agent tokens on Bloom search/read APIs. + +## Acceptance + +- Focused tests prove allowed AI-agent tokens can read only approved Bloom search/detail endpoints. +- Mutating endpoints and non-allowlisted reads reject AI-agent tokens. +- Access-log tests prove actor/IP/request/token provenance is present and sensitive values are redacted. diff --git a/pyproject.toml b/pyproject.toml index 65559a0..f3fff21 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,7 +28,7 @@ license = {text = "MIT"} requires-python = ">=3.12" dependencies = [ "cli-core-yo==2.1.1", - "daylily-tapdb>=7.0.5,<8.0.0", + "daylily-tapdb==8.0.1", "daylily-auth-cognito==2.1.5", "IPython>=8.18.1", "bandit[toml]>=1.8.0", diff --git a/static/js/graph.js b/static/js/graph.js index 9ebbb86..b6eae15 100644 --- a/static/js/graph.js +++ b/static/js/graph.js @@ -27,6 +27,7 @@ const keyState = { c: false, n: false, i: false, + z: false, }; const DEFAULT_CONTROL_STATE = { @@ -160,13 +161,13 @@ const cytoscapeStyle = [ "width": 2, "line-color": "#666", "curve-style": "bezier", - "source-arrow-shape": "none", - "target-arrow-shape": "triangle", - "target-arrow-fill": "filled", - "target-arrow-color": "#666", + "source-arrow-shape": "triangle", + "source-arrow-fill": "filled", + "source-arrow-color": "#666", + "target-arrow-shape": "none", "source-endpoint": "outside-to-node", "target-endpoint": "outside-to-node", - "target-distance-from-node": 6, + "source-distance-from-node": 6, "arrow-scale": 1.6, "opacity": 1, }, @@ -176,7 +177,7 @@ const cytoscapeStyle = [ style: { "line-style": "dashed", "line-color": "#c1a967", - "target-arrow-color": "#c1a967", + "source-arrow-color": "#c1a967", }, }, { @@ -184,7 +185,7 @@ const cytoscapeStyle = [ style: { "line-style": "dotted", "line-color": "#f7c948", - "target-arrow-color": "#f7c948", + "source-arrow-color": "#f7c948", "width": 3, }, }, @@ -192,7 +193,7 @@ const cytoscapeStyle = [ selector: "edge:selected", style: { "line-color": "#e74c3c", - "target-arrow-color": "#e74c3c", + "source-arrow-color": "#e74c3c", "width": 3, }, }, @@ -385,6 +386,9 @@ function installKeyboardHandlers() { if (key === "i") { keyState.i = true; } + if (key === "z") { + keyState.z = true; + } if (key === "escape") { clearPendingLineageSelection(); setStatus("Cleared selection.", "warn"); @@ -411,9 +415,30 @@ function installKeyboardHandlers() { if (key === "i") { keyState.i = false; } + if (key === "z") { + keyState.z = false; + } }); } +function configureCytoscapeInteractions(container) { + if (container.dataset.cytoscapeWheelGate === "installed") { + return; + } + container.dataset.cytoscapeWheelGate = "installed"; + container.addEventListener( + "wheel", + (evt) => { + const isPinchZoom = evt.ctrlKey || evt.metaKey; + if (isPinchZoom || keyState.z) { + return; + } + evt.stopImmediatePropagation(); + }, + { capture: true, passive: true }, + ); +} + function registerTapSequence(nodeId, button) { const key = `${nodeId}|${button}`; const now = Date.now(); @@ -1081,6 +1106,7 @@ function initCytoscape(container, elements) { evt.preventDefault(); }); + configureCytoscapeInteractions(container); cy = cytoscape({ container: container, elements: elements, diff --git a/static/modern/css/bloom_modern.css b/static/modern/css/bloom_modern.css index 3b9e612..294a908 100644 --- a/static/modern/css/bloom_modern.css +++ b/static/modern/css/bloom_modern.css @@ -1121,3 +1121,96 @@ pre { white-space: nowrap; border-width: 0; } +.lsmc-theme-control, +.lsmc-action-help-button, +.lsmc-action-help-panel { + font-family: var(--font-sans, Inter, system-ui, sans-serif); + z-index: 2147483000; +} + +.lsmc-theme-control { + position: fixed; + right: 1rem; + bottom: 5rem; + padding: 0.4rem 0.55rem; + border: 1px solid color-mix(in srgb, currentColor 20%, transparent); + border-radius: 8px; + background: color-mix(in srgb, Canvas 94%, transparent); + box-shadow: 0 10px 28px rgba(15, 23, 42, 0.16); + font-size: 0.78rem; +} + +.lsmc-theme-control label { + display: flex; + gap: 0.4rem; + align-items: center; +} + +.lsmc-theme-control select { + min-height: 1.7rem; + border-radius: 6px; +} + +.lsmc-action-help-button { + position: fixed; + right: 1rem; + bottom: 1rem; + width: 2.65rem; + height: 2.65rem; + border: 0; + border-radius: 999px; + background: #1f6feb; + color: white; + font-weight: 800; + box-shadow: 0 12px 30px rgba(15, 23, 42, 0.22); +} + +.lsmc-action-help-panel { + position: fixed; + right: 1rem; + bottom: 4.1rem; + width: min(26rem, calc(100vw - 2rem)); + padding: 0.8rem; + border: 1px solid color-mix(in srgb, currentColor 20%, transparent); + border-radius: 8px; + background: Canvas; + color: CanvasText; + box-shadow: 0 18px 44px rgba(15, 23, 42, 0.24); +} + +.lsmc-action-help-panel pre { + overflow: auto; + margin: 0.55rem 0; + padding: 0.65rem; + border-radius: 6px; + background: color-mix(in srgb, CanvasText 8%, Canvas); + white-space: pre-wrap; +} + +html[data-theme="lsmc"] body { + background: #f4f8fb; + color: #172033; +} + +html[data-theme="dark"] { + color-scheme: dark; +} + +html[data-theme="dark"] body { + background: #10141d; + color: #e5edf7; +} + +html[data-theme="light"] body { + background: #ffffff; + color: #111827; +} + +html[data-theme="tacky"] body { + background: #fff700; + color: #1f1147; +} + +html[data-theme="tacky"] .lsmc-action-help-button { + background: #ff00b8; +} diff --git a/static/modern/js/lsmc_ui.js b/static/modern/js/lsmc_ui.js new file mode 100644 index 0000000..d2e2a7c --- /dev/null +++ b/static/modern/js/lsmc_ui.js @@ -0,0 +1,74 @@ +(function () { + const themes = ["original", "lsmc", "dark", "light", "tacky"]; + const storageKey = "lsmc.ui.theme"; + + function currentTheme() { + const stored = window.localStorage.getItem(storageKey); + return themes.includes(stored) ? stored : "original"; + } + + function applyTheme(theme) { + const value = themes.includes(theme) ? theme : "original"; + document.documentElement.dataset.theme = value; + window.localStorage.setItem(storageKey, value); + } + + function commandForPage() { + const explicit = document.body.dataset.actionHelpCommand || ""; + if (explicit) return explicit; + if (location.pathname.startsWith("/search")) return "bloom search --help"; + if (location.pathname.startsWith("/create_object")) return "bloom object create --help"; + if (location.pathname.startsWith("/admin")) return "bloom admin --help"; + if (location.pathname.startsWith("/dag")) return "bloom dag show --help"; + return `No CLI equivalent for bloom ${location.pathname}`; + } + + function initThemeControl() { + const wrap = document.createElement("div"); + wrap.className = "lsmc-theme-control"; + const label = document.createElement("label"); + label.textContent = "Theme"; + const select = document.createElement("select"); + for (const theme of themes) { + const option = document.createElement("option"); + option.value = theme; + option.textContent = theme; + select.appendChild(option); + } + select.value = currentTheme(); + select.addEventListener("change", () => applyTheme(select.value)); + label.appendChild(select); + wrap.appendChild(label); + document.body.appendChild(wrap); + } + + function initActionHelp() { + const button = document.createElement("button"); + button.type = "button"; + button.className = "lsmc-action-help-button"; + button.setAttribute("aria-expanded", "false"); + button.textContent = "?"; + const panel = document.createElement("aside"); + panel.className = "lsmc-action-help-panel"; + panel.hidden = true; + panel.innerHTML = 'Action Help
';
+    const output = panel.querySelector("pre");
+    const copy = panel.querySelector("button");
+    function refresh() {
+      output.textContent = commandForPage();
+    }
+    button.addEventListener("click", () => {
+      panel.hidden = !panel.hidden;
+      button.setAttribute("aria-expanded", String(!panel.hidden));
+      refresh();
+    });
+    copy.addEventListener("click", () => navigator.clipboard?.writeText(output.textContent || ""));
+    document.body.append(button, panel);
+  }
+
+  applyTheme(currentTheme());
+  document.addEventListener("DOMContentLoaded", () => {
+    initThemeControl();
+    initActionHelp();
+  });
+})();
diff --git a/templates/modern/base.html b/templates/modern/base.html
index ecdb0da..5fafe55 100644
--- a/templates/modern/base.html
+++ b/templates/modern/base.html
@@ -1,5 +1,5 @@
 
-
+
 
     
     
@@ -156,6 +156,7 @@
     
     
     
+    
 
     
     
+{% endblock %}
diff --git a/tests/test_bloom_prefix_taxonomy.py b/tests/test_bloom_prefix_taxonomy.py
index 856a4ff..12b3181 100644
--- a/tests/test_bloom_prefix_taxonomy.py
+++ b/tests/test_bloom_prefix_taxonomy.py
@@ -62,6 +62,7 @@ def test_wet_lab_templates_use_bloom_prefix_taxonomy() -> None:
         "data/library-index-assignment/sequencing-library/1.0": "BDA",
         "data/execution/transfer/1.0": "BDT",
         "generic/generic/external_object_link/1.0": "BGX",
+        "set/run-set/generic/1.01": "BGS",
     }
 
     for code, expected_prefix in expected_prefixes.items():
diff --git a/tests/test_lab_actions_api.py b/tests/test_lab_actions_api.py
new file mode 100644
index 0000000..b5f3953
--- /dev/null
+++ b/tests/test_lab_actions_api.py
@@ -0,0 +1,566 @@
+"""API coverage for Bloom lab actions."""
+
+from __future__ import annotations
+
+import os
+from unittest.mock import patch
+
+os.environ["BLOOM_DEV_AUTH_BYPASS"] = "true"
+os.environ["BLOOM_OAUTH"] = "no"
+
+from fastapi.testclient import TestClient
+
+from main import app
+
+
+def _client() -> TestClient:
+    return TestClient(app)
+
+
+def _create_object(
+    client: TestClient,
+    *,
+    category: str,
+    type_name: str,
+    subtype: str,
+    name: str,
+    version: str = "1.0",
+    properties: dict | None = None,
+    count: int = 1,
+) -> dict:
+    response = client.post(
+        "/api/v1/object-creation/create",
+        json={
+            "category": category,
+            "type": type_name,
+            "subtype": subtype,
+            "version": version,
+            "name": name,
+            "properties": properties or {},
+            "count": count,
+        },
+    )
+    assert response.status_code == 200, response.text
+    return response.json()
+
+
+def _link_material(client: TestClient, *, container_euid: str, content_euid: str) -> None:
+    response = client.post(
+        "/api/v1/lineages/",
+        json={
+            "parent_euid": container_euid,
+            "child_euid": content_euid,
+            "relationship_type": "HOLDS_MATERIAL",
+        },
+    )
+    assert response.status_code == 200, response.text
+
+
+def _create_filled_tube(client: TestClient, *, suffix: str) -> tuple[str, str]:
+    with patch(
+        "bloom_lims.integrations.atlas.events.emit_bloom_event", return_value=None
+    ):
+        tube = _create_object(
+            client,
+            category="container",
+            type_name="tube",
+            subtype="tube-generic-10ml",
+            name=f"pytest incoming tube {suffix}",
+        )
+    content = _create_object(
+        client,
+        category="content",
+        type_name="specimen",
+        subtype="buccal-swab",
+        name=f"pytest buccal specimen {suffix}",
+    )
+    _link_material(client, container_euid=tube["euid"], content_euid=content["euid"])
+    return tube["euid"], content["euid"]
+
+
+def _create_plate(client: TestClient, *, name: str) -> str:
+    with patch(
+        "bloom_lims.integrations.atlas.events.emit_bloom_event", return_value=None
+    ):
+        plate = _create_object(
+            client,
+            category="container",
+            type_name="plate",
+            subtype="fixed-plate-96",
+            name=name,
+        )
+    return plate["euid"]
+
+
+def _create_reagent_index(client: TestClient, *, name: str) -> str:
+    reagent = _create_object(
+        client,
+        category="content",
+        type_name="reagent",
+        subtype="sequencing-index",
+        name=name,
+    )
+    return reagent["euid"]
+
+
+def _create_instrument(client: TestClient, *, name: str) -> str:
+    instrument = _create_object(
+        client,
+        category="equipment",
+        type_name="sequencers",
+        subtype="novaseq-6000",
+        name=name,
+    )
+    return instrument["euid"]
+
+
+def test_lab_actions_full_ilmn_flow_and_csv_export() -> None:
+    client = _client()
+    tube_1, _ = _create_filled_tube(client, suffix="a")
+    tube_2, _ = _create_filled_tube(client, suffix="b")
+
+    with patch(
+        "bloom_lims.integrations.atlas.events.emit_bloom_event", return_value=None
+    ):
+        extraction = client.post(
+            "/api/v1/lab-actions/extraction-plates",
+            json={
+                "mode": "auto",
+                "tube_euids": [tube_1, tube_2],
+                "plate_name": "pytest extraction plate",
+                "create_run_set": True,
+            },
+        )
+    assert extraction.status_code == 200, extraction.text
+    extraction_payload = extraction.json()
+    assert extraction_payload["plate_euid"]
+    assert extraction_payload["run_set_euid"]
+    assert [item["well_name"] for item in extraction_payload["mappings"]] == [
+        "A1",
+        "A2",
+    ]
+    assert all(item["output_content_euid"] for item in extraction_payload["mappings"])
+
+    plate_csv = client.get(
+        f"/api/v1/lab-actions/plates/{extraction_payload['plate_euid']}/mapping.csv"
+    )
+    assert plate_csv.status_code == 200, plate_csv.text
+    assert "tube_euid,plate_euid,well_euid,well_row,well_col" in plate_csv.text
+    assert tube_1 in plate_csv.text
+
+    with patch(
+        "bloom_lims.integrations.atlas.events.emit_bloom_event", return_value=None
+    ):
+        library = client.post(
+            "/api/v1/lab-actions/seq-library-plates",
+            json={
+                "mode": "plate_1_to_1",
+                "source_plate_euid": extraction_payload["plate_euid"],
+                "plate_name": "pytest library plate",
+            },
+        )
+    assert library.status_code == 200, library.text
+    library_payload = library.json()
+    assert library_payload["plate_euid"]
+    assert len(library_payload["mappings"]) == 2
+    library_contents = [
+        item["library_content_euid"] for item in library_payload["mappings"]
+    ]
+
+    with patch(
+        "bloom_lims.integrations.atlas.events.emit_bloom_event", return_value=None
+    ):
+        pool = client.post(
+            "/api/v1/lab-actions/seq-library-pools",
+            json={
+                "input_euids": library_contents,
+                "platform": "ILMN",
+                "pool_name": "pytest sequencing pool",
+            },
+        )
+    assert pool.status_code == 200, pool.text
+    pool_payload = pool.json()
+    assert pool_payload["pool_tube_euid"]
+    assert pool_payload["pool_content_euid"]
+    assert pool_payload["member_euids"] == library_contents
+
+    seq_run = client.post(
+        "/api/v1/lab-actions/seq-runs",
+        json={
+            "pool_tube_euid": pool_payload["pool_tube_euid"],
+            "pool_content_euid": pool_payload["pool_content_euid"],
+            "platform": "ILMN",
+            "operator": "pytest@example.com",
+            "flowcell_barcode": "PYTEST-FLOWCELL",
+            "status": "created",
+        },
+    )
+    assert seq_run.status_code == 200, seq_run.text
+    run_payload = seq_run.json()
+    assert run_payload["set_euid"]
+
+    sample_sheet = client.get(
+        f"/api/v1/lab-actions/seq-runs/{run_payload['set_euid']}/samplesheet"
+    )
+    assert sample_sheet.status_code == 200, sample_sheet.text
+    assert "[Header]" in sample_sheet.text
+    assert f"RunSetEUID,{run_payload['set_euid']}" in sample_sheet.text
+    assert "PYTEST-FLOWCELL" in sample_sheet.text
+    for library_content in library_contents:
+        assert library_content in sample_sheet.text
+
+
+def test_lab_actions_validation_and_non_ilmn_samplesheet_rejection() -> None:
+    client = _client()
+    invalid = client.post(
+        "/api/v1/lab-actions/extraction-plates",
+        json={"mode": "auto", "tube_euids": []},
+    )
+    assert invalid.status_code == 422
+
+    tube, _ = _create_filled_tube(client, suffix="non-ilmn")
+    with patch(
+        "bloom_lims.integrations.atlas.events.emit_bloom_event", return_value=None
+    ):
+        pool = client.post(
+            "/api/v1/lab-actions/seq-library-pools",
+            json={
+                "input_euids": [tube],
+                "platform": "ONT",
+                "pool_name": "pytest ont pool",
+            },
+        )
+    assert pool.status_code == 200, pool.text
+    run = client.post(
+        "/api/v1/lab-actions/seq-runs",
+        json={
+            "pool_tube_euid": pool.json()["pool_tube_euid"],
+            "pool_content_euid": pool.json()["pool_content_euid"],
+            "platform": "ONT",
+            "flowcell_barcode": "ONT-FLOWCELL",
+        },
+    )
+    assert run.status_code == 200, run.text
+    sample_sheet = client.get(
+        f"/api/v1/lab-actions/seq-runs/{run.json()['set_euid']}/samplesheet"
+    )
+    assert sample_sheet.status_code == 400
+    assert "only implemented for ILMN" in sample_sheet.json()["detail"]
+
+
+def test_object_creation_count_and_print_euid_mock() -> None:
+    client = _client()
+    created = _create_object(
+        client,
+        category="set",
+        type_name="run-set",
+        subtype="generic",
+        version="1.01",
+        name="pytest run set",
+        count=3,
+    )
+    assert len(created["created_euids"]) == 3
+    assert created["euid"] == created["created_euids"][0]
+
+    with patch("bloom_lims.domain.lab_actions.ZebraDayService") as service_cls:
+        service = service_cls.return_value
+        service.submit_print_job.side_effect = [
+            {"job_euid": f"JOB-{index}", "status": "queued"} for index in range(3)
+        ]
+        response = client.post(
+            "/api/v1/lab-actions/print-euids",
+            json={
+                "euids": created["created_euids"],
+                "lab": "SSF",
+                "printer_id": "pytest-printer",
+                "label_zpl_style": "euid",
+                "copies": 1,
+            },
+        )
+    assert response.status_code == 200, response.text
+    assert response.json()["printed"] == 3
+    assert service.submit_print_job.call_count == 3
+
+    recursive_batch = client.post(
+        "/api/v1/object-creation/create",
+        json={
+            "category": "container",
+            "type": "plate",
+            "subtype": "fixed-plate-96",
+            "version": "1.0",
+            "name": "unsafe recursive plate batch",
+            "count": 2,
+        },
+    )
+    assert recursive_batch.status_code == 400
+    assert "recursive templates" in recursive_batch.json()["detail"]
+
+
+def test_lab_actions_gui_renders_wizard() -> None:
+    client = _client()
+    response = client.get("/lab-actions")
+    assert response.status_code == 200, response.text
+    html = response.text
+    assert "Lab Actions" in html
+    assert "Extraction Plate" in html
+    assert "Sequencing-Library Plate" in html
+    assert "Sequencing Pool Tube" in html
+    assert "Sequencing Run Set" in html
+    assert "/api/v1/lab-actions/extraction-plates" in html
+
+
+def test_directed_extraction_into_existing_plate_with_quant_and_reuse_guard() -> None:
+    client = _client()
+    existing_plate_euid = _create_plate(client, name="pytest existing extraction plate")
+    tube, _ = _create_filled_tube(client, suffix="directed")
+
+    with patch(
+        "bloom_lims.integrations.atlas.events.emit_bloom_event", return_value=None
+    ):
+        response = client.post(
+            "/api/v1/lab-actions/extraction-plates",
+            json={
+                "mode": "directed",
+                "plate_euid": existing_plate_euid,
+                "assignments": [
+                    {
+                        "tube_euid": tube,
+                        "row": "B",
+                        "col": 3,
+                        "quant": {
+                            "method": "Qubit",
+                            "concentration": 42.5,
+                            "concentration_units": "ng/uL",
+                        },
+                    }
+                ],
+                "run_set": {
+                    "name": "pytest directed extraction set",
+                    "members": [tube],
+                    "external_members": ["atlas:pytest-external-member"],
+                    "metadata": {"purpose": "directed-test"},
+                },
+            },
+        )
+    assert response.status_code == 200, response.text
+    payload = response.json()
+    assert payload["plate_euid"] == existing_plate_euid
+    assert payload["new_container_euids"] == []
+    assert payload["run_set_euid"]
+    assert payload["mappings"][0]["well_name"] == "B3"
+    assert payload["mappings"][0]["quant_euid"]
+
+    repeat = client.post(
+        "/api/v1/lab-actions/extraction-plates",
+        json={
+            "mode": "directed",
+            "plate_euid": existing_plate_euid,
+            "assignments": [{"tube_euid": tube, "row": "B", "col": 3}],
+        },
+    )
+    assert repeat.status_code == 400
+    assert "already filled" in repeat.json()["detail"]
+
+
+def test_directed_extraction_rejects_duplicate_tubes_and_wells() -> None:
+    client = _client()
+    tube_1, _ = _create_filled_tube(client, suffix="dup-1")
+    tube_2, _ = _create_filled_tube(client, suffix="dup-2")
+
+    duplicate_tube = client.post(
+        "/api/v1/lab-actions/extraction-plates",
+        json={
+            "mode": "directed",
+            "assignments": [
+                {"tube_euid": tube_1, "row": "A", "col": 1},
+                {"tube_euid": tube_1, "row": "A", "col": 2},
+            ],
+        },
+    )
+    assert duplicate_tube.status_code == 400
+    assert "duplicate assignment tube_euid" in duplicate_tube.json()["detail"]
+
+    duplicate_well = client.post(
+        "/api/v1/lab-actions/extraction-plates",
+        json={
+            "mode": "directed",
+            "assignments": [
+                {"tube_euid": tube_1, "row": "A", "col": 1},
+                {"tube_euid": tube_2, "row": "A", "col": 1},
+            ],
+        },
+    )
+    assert duplicate_well.status_code == 400
+    assert "duplicate destination well" in duplicate_well.json()["detail"]
+
+
+def test_directed_library_plate_with_index_and_run_set() -> None:
+    client = _client()
+    tube, _ = _create_filled_tube(client, suffix="library-directed")
+    extraction = client.post(
+        "/api/v1/lab-actions/extraction-plates",
+        json={"mode": "auto", "tube_euids": [tube]},
+    )
+    assert extraction.status_code == 200, extraction.text
+    source_well = extraction.json()["mappings"][0]["well_euid"]
+    index_euid = _create_reagent_index(client, name="pytest sequencing index")
+
+    with patch(
+        "bloom_lims.integrations.atlas.events.emit_bloom_event", return_value=None
+    ):
+        response = client.post(
+            "/api/v1/lab-actions/seq-library-plates",
+            json={
+                "mode": "directed",
+                "plate_name": "pytest directed library plate",
+                "assignments": [
+                    {
+                        "source_well_euid": source_well,
+                        "row": "C",
+                        "col": 4,
+                        "index_barcode": "ACGTACGT",
+                        "index_euid": index_euid,
+                        "data": {"cycles": 8},
+                    }
+                ],
+                "create_run_set": True,
+                "run_set": {"name": "pytest library run set"},
+            },
+        )
+    assert response.status_code == 200, response.text
+    payload = response.json()
+    assert payload["run_set_euid"]
+    assert payload["mappings"][0]["well_name"] == "C4"
+    assert payload["mappings"][0]["index_barcode"] == "ACGTACGT"
+    assert payload["mappings"][0]["index_euid"] == index_euid
+
+    duplicate_destination = client.post(
+        "/api/v1/lab-actions/seq-library-plates",
+        json={
+            "mode": "directed",
+            "assignments": [
+                {"source_well_euid": source_well, "row": "A", "col": 1},
+                {"source_well_euid": source_well, "row": "A", "col": 1},
+            ],
+        },
+    )
+    assert duplicate_destination.status_code == 400
+    assert "duplicate destination well" in duplicate_destination.json()["detail"]
+
+
+def test_pool_existing_tube_pool_from_pool_and_seq_run_links() -> None:
+    client = _client()
+    tube, _ = _create_filled_tube(client, suffix="pool-existing")
+    extraction = client.post(
+        "/api/v1/lab-actions/extraction-plates",
+        json={"mode": "auto", "tube_euids": [tube]},
+    )
+    assert extraction.status_code == 200, extraction.text
+    library = client.post(
+        "/api/v1/lab-actions/seq-library-plates",
+        json={
+            "mode": "plate_1_to_1",
+            "source_plate_euid": extraction.json()["plate_euid"],
+        },
+    )
+    assert library.status_code == 200, library.text
+    library_content = library.json()["mappings"][0]["library_content_euid"]
+
+    existing_pool_tube = _create_object(
+        client,
+        category="container",
+        type_name="tube",
+        subtype="tube-generic-10ml",
+        name="pytest existing pool tube",
+    )["euid"]
+    first_pool = client.post(
+        "/api/v1/lab-actions/seq-library-pools",
+        json={
+            "input_euids": [library_content],
+            "pool_tube_euid": existing_pool_tube,
+            "platform": "ILMN",
+            "pool_name": "pytest first pool",
+            "create_run_set": True,
+        },
+    )
+    assert first_pool.status_code == 200, first_pool.text
+    first_payload = first_pool.json()
+    assert first_payload["pool_tube_euid"] == existing_pool_tube
+    assert first_payload["new_container_euids"] == []
+    assert first_payload["run_set_euid"]
+
+    second_pool = client.post(
+        "/api/v1/lab-actions/seq-library-pools",
+        json={
+            "input_euids": [first_payload["pool_tube_euid"]],
+            "platform": "ILMN",
+            "pool_name": "pytest pool from pool",
+        },
+    )
+    assert second_pool.status_code == 200, second_pool.text
+    assert second_pool.json()["member_euids"] == [first_payload["pool_content_euid"]]
+
+    duplicate_inputs = client.post(
+        "/api/v1/lab-actions/seq-library-pools",
+        json={
+            "input_euids": [library_content, library_content],
+            "platform": "ILMN",
+        },
+    )
+    assert duplicate_inputs.status_code == 400
+    assert "duplicate input_euids" in duplicate_inputs.json()["detail"]
+
+    instrument_euid = _create_instrument(client, name="pytest novaseq")
+    reagent_euid = _create_reagent_index(client, name="pytest run reagent")
+    seq_run = client.post(
+        "/api/v1/lab-actions/seq-runs",
+        json={
+            "pool_tube_euid": second_pool.json()["pool_tube_euid"],
+            "platform": "ILMN",
+            "operator": "pytest@example.com",
+            "instrument_euid": instrument_euid,
+            "machine": "NovaSeq 6000",
+            "flowcell_barcode": "FLOWCELL-LINKS",
+            "reagent_euids": [reagent_euid],
+            "status": "running",
+            "metadata": {"purpose": "link coverage"},
+        },
+    )
+    assert seq_run.status_code == 200, seq_run.text
+    assert seq_run.json()["status"] == "running"
+
+
+def test_lab_action_schema_validation_edges() -> None:
+    client = _client()
+    bad_auto = client.post(
+        "/api/v1/lab-actions/extraction-plates",
+        json={
+            "mode": "auto",
+            "tube_euids": ["Z-BCT-1"],
+            "assignments": [{"tube_euid": "Z-BCT-2", "row": "A", "col": 1}],
+        },
+    )
+    assert bad_auto.status_code == 422
+
+    bad_directed = client.post(
+        "/api/v1/lab-actions/extraction-plates",
+        json={"mode": "directed", "tube_euids": ["Z-BCT-1"]},
+    )
+    assert bad_directed.status_code == 422
+
+    bad_library = client.post(
+        "/api/v1/lab-actions/seq-library-plates",
+        json={"mode": "plate_1_to_1"},
+    )
+    assert bad_library.status_code == 422
+
+    too_many_prints = client.post(
+        "/api/v1/lab-actions/print-euids",
+        json={
+            "euids": [f"Z-BCT-{index}" for index in range(501)],
+            "lab": "SSF",
+            "printer_id": "pytest-printer",
+            "label_zpl_style": "euid",
+        },
+    )
+    assert too_many_prints.status_code == 422
diff --git a/tests/test_route_coverage_gaps_api.py b/tests/test_route_coverage_gaps_api.py
index e992fb4..f42f170 100644
--- a/tests/test_route_coverage_gaps_api.py
+++ b/tests/test_route_coverage_gaps_api.py
@@ -113,6 +113,45 @@ def test_object_creation_creates_all_sequencing_run_platform_prefixes(
         assert created["euid"].startswith(f"{domain_code}-{prefix}-")
 
 
+def test_object_creation_plate_creates_96_linked_wells(
+    client: TestClient, bdb
+) -> None:
+    created = _create_instance_via_object_creation(
+        client,
+        category="container",
+        type_name="plate",
+        subtype="fixed-plate-96",
+        version="1.0",
+        name="pytest-fixed-96",
+    )
+    plate_euid = created["euid"]
+
+    lineage_cls = bdb.Base.classes.generic_instance_lineage
+    instance_cls = bdb.Base.classes.generic_instance
+    plate = bdb.session.query(instance_cls).filter_by(euid=plate_euid).one()
+    lineages = (
+        bdb.session.query(lineage_cls)
+        .filter(
+            lineage_cls.parent_instance_uid == plate.uid,
+            lineage_cls.relationship_type == "contains",
+            lineage_cls.is_deleted.is_(False),
+        )
+        .all()
+    )
+    wells = [lineage.child_instance for lineage in lineages]
+    positions = {
+        ((well.json_addl or {}).get("cont_address") or {}).get("name")
+        for well in wells
+    }
+    assert len(wells) == 96
+    assert {well.type for well in wells} == {"well"}
+    assert {"A1", "H12"}.issubset(positions)
+
+    layout = client.get(f"/api/v1/containers/{plate_euid}/layout")
+    assert layout.status_code == 200, layout.text
+    assert layout.json()["well_count"] == 96
+
+
 def test_actions_endpoints_execute_handler_body(client: TestClient) -> None:
     resp = client.post(
         "/api/v1/actions/aliquot",
diff --git a/tests/test_template_instantiation_recursion.py b/tests/test_template_instantiation_recursion.py
new file mode 100644
index 0000000..752c999
--- /dev/null
+++ b/tests/test_template_instantiation_recursion.py
@@ -0,0 +1,185 @@
+from __future__ import annotations
+
+import logging
+from types import SimpleNamespace
+
+import pytest
+
+from bloom_lims.domain.base import BloomObj
+
+
+class _FakeLineage:
+    def __init__(self, **kwargs):
+        self.__dict__.update(kwargs)
+
+
+class _FakeSession:
+    def __init__(self):
+        self.added = []
+        self.commit_count = 0
+
+    def add(self, obj):
+        self.added.append(obj)
+
+    def commit(self):
+        self.commit_count += 1
+
+
+def _template(euid, category, type_name, subtype, *, layouts=None):
+    return SimpleNamespace(
+        euid=euid,
+        uid=hash(euid) & 0xFFFF,
+        name=euid,
+        category=category,
+        type=type_name,
+        subtype=subtype,
+        version="1.0",
+        bstatus="active",
+        json_addl={"instantiation_layouts": layouts or {}},
+        polymorphic_discriminator=f"{category}_template",
+    )
+
+
+def _fake_bloom_obj(templates):
+    obj = BloomObj.__new__(BloomObj)
+    obj.logger = logging.getLogger("test-template-instantiation")
+    obj.session = _FakeSession()
+    obj.Base = SimpleNamespace(
+        classes=SimpleNamespace(generic_instance_lineage=_FakeLineage)
+    )
+    obj.domain_code = "Z"
+    created = {"count": 0, "instances": {}}
+    templates_by_euid = {template.euid: template for template in templates}
+
+    def get_by_euid(euid):
+        return templates_by_euid.get(euid) or created["instances"].get(euid)
+
+    def query_template_by_component_v2(category=None, type=None, subtype=None, version=None):
+        return [
+            template
+            for template in templates
+            if (category is None or template.category == category)
+            and (type is None or template.type == type)
+            and (subtype is None or template.subtype == subtype)
+            and (version is None or template.version == version)
+        ]
+
+    def create_instance(template_euid, json_addl_overrides=None):
+        template = templates_by_euid[template_euid]
+        created["count"] += 1
+        instance = SimpleNamespace(
+            uid=created["count"],
+            euid=f"I-{created['count']}",
+            name=(json_addl_overrides or {})
+            .get("properties", {})
+            .get("name", template.name),
+            category=template.category,
+            type=template.type,
+            subtype=template.subtype,
+            version=template.version,
+            bstatus=template.bstatus,
+            json_addl=json_addl_overrides or {},
+            polymorphic_discriminator=f"{template.category}_instance",
+        )
+        created["instances"][instance.euid] = instance
+        return instance
+
+    obj.get_by_euid = get_by_euid
+    obj.query_template_by_component_v2 = query_template_by_component_v2
+    obj.create_instance = create_instance
+    return obj
+
+
+def test_create_instances_recurses_nested_instantiation_layouts():
+    leaf = _template("TPL-LEAF", "content", "material", "leaf")
+    mid = _template(
+        "TPL-MID",
+        "container",
+        "well",
+        "middle",
+        layouts=[
+            {
+                "relationship_type": "HOLDS_MATERIAL",
+                "child_templates": [
+                    {
+                        "template_code": "content/material/leaf/1.0/",
+                        "json_addl": {"properties": {"name": "leaf child"}},
+                    }
+                ],
+            }
+        ],
+    )
+    root = _template(
+        "TPL-ROOT",
+        "container",
+        "plate",
+        "nested",
+        layouts=[
+            {
+                "relationship_type": "contains",
+                "child_templates": [
+                    {
+                        "template_code": "container/well/middle/1.0/",
+                        "json_addl": {"properties": {"name": "middle child"}},
+                    }
+                ],
+            }
+        ],
+    )
+    obj = _fake_bloom_obj([root, mid, leaf])
+
+    parent_rows, child_rows = obj.create_instances("TPL-ROOT")
+
+    assert len(parent_rows) == 1
+    assert len(child_rows) == 2
+    assert {child.type for child in child_rows} == {"well", "material"}
+    lineages = [
+        row for row in obj.session.added if isinstance(row, _FakeLineage)
+    ]
+    assert [row.relationship_type for row in lineages] == [
+        "HOLDS_MATERIAL",
+        "contains",
+    ]
+
+
+def test_create_instances_rejects_template_cycles():
+    cyclic = _template(
+        "TPL-CYCLE",
+        "container",
+        "plate",
+        "cycle",
+        layouts=[
+            {
+                "relationship_type": "contains",
+                "child_templates": [
+                    {"template_code": "container/plate/cycle/1.0/"}
+                ],
+            }
+        ],
+    )
+    obj = _fake_bloom_obj([cyclic])
+
+    with pytest.raises(Exception, match="cycle detected"):
+        obj.create_instances("TPL-CYCLE")
+
+
+def test_create_instances_enforces_object_count_limit():
+    child = _template("TPL-CHILD", "container", "well", "child")
+    root = _template(
+        "TPL-ROOT",
+        "container",
+        "plate",
+        "limited",
+        layouts=[
+            {
+                "relationship_type": "contains",
+                "child_templates": [
+                    {"template_code": "container/well/child/1.0/"}
+                ],
+            }
+        ],
+    )
+    obj = _fake_bloom_obj([root, child])
+
+    with pytest.raises(Exception, match="exceeded max object count 1"):
+        obj.create_instances("TPL-ROOT", max_instances=1)

From 62d060ccc5f6ad12c9f257ae6e9a024defd697af Mon Sep 17 00:00:00 2001
From: John Major 
Date: Thu, 18 Jun 2026 09:13:12 -0700
Subject: [PATCH 37/47] Refresh README current-state documentation

---
 README.md | 43 ++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 40 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 6f25162..51f11ea 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,50 @@
-# BLOOM
+

+
+██████╗ ██╗      ██████╗  ██████╗ ███╗   ███╗
+██╔══██╗██║     ██╔═══██╗██╔═══██╗████╗ ████║
+██████╔╝██║     ██║   ██║██║   ██║██╔████╔██║
+██╔══██╗██║     ██║   ██║██║   ██║██║╚██╔╝██║
+██████╔╝███████╗╚██████╔╝╚██████╔╝██║ ╚═╝ ██║
+╚═════╝ ╚══════╝ ╚═════╝  ╚═════╝ ╚═╝     ╚═╝
+

+
Internal material, container, lineage, and lab-action graph service.

+

+  Quickstart ·
+  API ·
+  GUI ·
+  Lab actions ·
+  Tests
+

+

 
 ## Overview
 
 Bloom is the LSMC internal material and container graph service. It owns laboratory containers, materials/content, equipment, lineage, recursive template creation, search, and graph views. Atlas owns orders and customer-facing accession context; Bloom owns the physical/material execution graph.
 
-Current Dayhoff pin: `7.0.14`. Current TapDB dependency: `daylily-tapdb @ ...@9.0.4`.
+Current Dayhoff pin: `7.0.16`. Current TapDB dependency: `daylily-tapdb @ ...@9.0.5`.
 
 Bloom is internal-only in Dayhoff exposure policy. It must be reachable only through approved LSMC networks and Dayhoff-generated service credentials.
 
+## What It Does
+
+- Owns Bloom containers, materials/content, equipment, recursive templates, lineages, search, and graph views.
+- Exposes `/lab-actions` and `/api/v1/lab-actions/*` for extraction plate, sequencing-library plate, pool-tube, and sequencing-run setup.
+- Mounts TapDB at `/tapdb` for generic object, template, lineage, audit, graph, and external-link inspection.
+- Provides health and observability surfaces for Kahlo and Dayhoff deployment verification.
+
+## How It Works
+
+```mermaid
+flowchart LR
+    Tube["Incoming tube + content"] --> Extraction["Extraction plate + gDNA"]
+    Extraction --> Library["Sequencing-library plate"]
+    Library --> Pool["Pool tube + pool content"]
+    Pool --> RunSet["Sequencing run set"]
+    RunSet --> OWY["Samplesheet for OWY/Kahlo traceability"]
+```
+
+Bloom models physical/material execution. Atlas owns orders and customer accession context; Dewey owns durable artifact identity; Ursa owns analysis trigger/job records.
+
 ## Quickstart
 
 ```bash
@@ -76,7 +113,7 @@ python -m pytest tests -q
 python -m pytest tests/test_lsmc_ui_skin_system_contract.py -q
 ```
 
-Deployed browser evidence should target `https://bloom..dev.lsmc.bio` and include the dashboard, object search/detail, TapDB mount, graph, and auth redirect surfaces. Current committed `jemdev5` evidence is linked from Dayhoff `docs/releases/dayhoff_7_0_61_jemdev5_evidence/`.
+Deployed browser evidence should target `https://bloom..dev.lsmc.bio` and include the dashboard, object search/detail, TapDB mount, graph, and auth redirect surfaces. Current `jemdev5` deployment evidence is linked from Dayhoff `docs/plans/20260618T132900Z_jemdev5_dayhoff_7067_live_deploy_ledger.md`.
 
 ## Technical Details, History, And Linkouts
 

From 8b64cad18e4c496be2fc46afee5a543f54ce0622 Mon Sep 17 00:00:00 2001
From: John Major 
Date: Thu, 18 Jun 2026 09:34:08 -0700
Subject: [PATCH 38/47] Add lab-action spreadsheet upload flows

---
 README.md                                     |  10 +-
 bloom_lims/api/v1/lab_actions.py              |  97 ++-
 bloom_lims/domain/lab_action_spreadsheets.py  | 193 ++++++
 bloom_lims/domain/lab_actions.py              | 563 +++++++++++++++++-
 bloom_lims/schemas/lab_actions.py             | 103 ++++
 docs/apis.md                                  |   6 +
 docs/gui.md                                   |   4 +
 docs/lab_actions.md                           | 127 +++-
 ...om_lab_action_spreadsheet_upload_ledger.md |  75 +++
 templates/modern/lab_actions.html             | 151 ++++-
 tests/test_lab_actions_api.py                 | 303 ++++++++++
 11 files changed, 1615 insertions(+), 17 deletions(-)
 create mode 100644 bloom_lims/domain/lab_action_spreadsheets.py
 create mode 100644 docs/plans/20260618T190000Z_bloom_lab_action_spreadsheet_upload_ledger.md

diff --git a/README.md b/README.md
index 51f11ea..b337713 100644
--- a/README.md
+++ b/README.md
@@ -80,7 +80,7 @@ For normal user/admin behavior, the CLI, API, and GUI are alternate surfaces ove
 
 Bloom exposes a FastAPI/Jinja GUI for internal operators. Current surfaces include dashboard/home, object search and details, container/content/equipment operations, graph views, auth/profile flows, the `/lab-actions` wet-lab action wizard, and the mounted TapDB GUI at `/tapdb` when configured by Dayhoff.
 
-`/lab-actions` is the temporary operator flow for mapping incoming biospecimen tubes to extraction plates, sequencing-library plates, pool tubes, and sequencing run sets. It is backed by `/api/v1/lab-actions/*`; GUI actions should not have behavior that is unavailable through the API.
+`/lab-actions` is the temporary operator flow for mapping incoming biospecimen tubes to extraction plates, extraction QC plates, sequencing-library plates, pool tubes, generic lab/run sets, per-well associated data, and sequencing run sets. It also accepts `.csv` and `.xlsx` spreadsheet uploads for the same API-backed actions. GUI actions should not have behavior that is unavailable through the API.
 
 See [`docs/lab_actions.md`](docs/lab_actions.md) for the template matrix, lineage contract, API examples, GUI flow, and production rollout checklist for this surface.
 
@@ -93,9 +93,15 @@ The primary API is under `/api/v1/*`. Current route families include objects, co
 The lab-action route family includes:
 
 - `POST /api/v1/lab-actions/extraction-plates`
+- `POST /api/v1/lab-actions/extraction-qc-plates`
 - `POST /api/v1/lab-actions/seq-library-plates`
 - `POST /api/v1/lab-actions/seq-library-pools`
 - `POST /api/v1/lab-actions/seq-runs`
+- `POST /api/v1/lab-actions/sets`
+- `GET /api/v1/lab-actions/sets/{set_euid}`
+- `POST /api/v1/lab-actions/sets/{set_euid}/members`
+- `POST /api/v1/lab-actions/plate-well-data`
+- `POST /api/v1/lab-actions/spreadsheet-import`
 - `GET /api/v1/lab-actions/seq-runs/{set_euid}/samplesheet`
 - `GET /api/v1/lab-actions/plates/{plate_euid}/mapping.csv`
 - `POST /api/v1/lab-actions/print-euids`
@@ -119,7 +125,7 @@ Deployed browser evidence should target `https://bloom..dev.lsmc.bio` an
 
 - [`docs/apis.md`](docs/apis.md): API details.
 - [`docs/gui.md`](docs/gui.md): GUI routes and screenshots when current.
-- [`docs/lab_actions.md`](docs/lab_actions.md): extraction/library/pooling/sequencing-run action flow, template matrix, and production rollout checklist.
+- [`docs/lab_actions.md`](docs/lab_actions.md): extraction/QC/library/pooling/set/sequencing-run action flow, spreadsheet upload schemas, template matrix, and production rollout checklist.
 - [`docs/architecture.md`](docs/architecture.md): domain model and runtime boundaries.
 - [`docs/becoming_a_discoverable_service.md`](docs/becoming_a_discoverable_service.md): Dayhoff/Kahlo observability contract.
 - [`docs/plans/`](docs/plans/): active ledgers.
diff --git a/bloom_lims/api/v1/lab_actions.py b/bloom_lims/api/v1/lab_actions.py
index 0296c8a..591a32e 100644
--- a/bloom_lims/api/v1/lab_actions.py
+++ b/bloom_lims/api/v1/lab_actions.py
@@ -4,12 +4,16 @@
 
 import logging
 
-from fastapi import APIRouter, Depends, HTTPException
+from fastapi import APIRouter, Depends, File, HTTPException, Query, UploadFile
 from fastapi.responses import PlainTextResponse
 
 from bloom_lims.domain.lab_actions import LabActionsService
 from bloom_lims.schemas.lab_actions import (
     ExtractionPlateRequest,
+    ExtractionQcPlateRequest,
+    LabSetMembersRequest,
+    LabSetRequest,
+    PlateWellDataRequest,
     PrintEuidRequest,
     SeqLibraryPlateRequest,
     SeqLibraryPoolRequest,
@@ -53,6 +57,34 @@ async def create_extraction_plate(
         service.close()
 
 
+@router.post("/extraction-qc-plates")
+async def fill_extraction_qc_plate(
+    payload: ExtractionQcPlateRequest,
+    user: APIUser = Depends(require_write),
+):
+    service = _service_for_user(user)
+    try:
+        return service.fill_extraction_qc_plate(payload)
+    except Exception as exc:
+        _raise_http(exc)
+    finally:
+        service.close()
+
+
+@router.post("/plate-well-data")
+async def attach_plate_well_data(
+    payload: PlateWellDataRequest,
+    user: APIUser = Depends(require_write),
+):
+    service = _service_for_user(user)
+    try:
+        return service.attach_plate_well_data(payload)
+    except Exception as exc:
+        _raise_http(exc)
+    finally:
+        service.close()
+
+
 @router.post("/seq-library-plates")
 async def create_seq_library_plate(
     payload: SeqLibraryPlateRequest,
@@ -95,6 +127,49 @@ async def create_seq_run_set(
         service.close()
 
 
+@router.post("/sets")
+async def create_lab_set(
+    payload: LabSetRequest,
+    user: APIUser = Depends(require_write),
+):
+    service = _service_for_user(user)
+    try:
+        return service.create_lab_set(payload)
+    except Exception as exc:
+        _raise_http(exc)
+    finally:
+        service.close()
+
+
+@router.get("/sets/{set_euid}")
+async def get_lab_set(
+    set_euid: str,
+    user: APIUser = Depends(require_read),
+):
+    service = _service_for_user(user)
+    try:
+        return service.get_lab_set(set_euid)
+    except Exception as exc:
+        _raise_http(exc)
+    finally:
+        service.close()
+
+
+@router.post("/sets/{set_euid}/members")
+async def add_lab_set_members(
+    set_euid: str,
+    payload: LabSetMembersRequest,
+    user: APIUser = Depends(require_write),
+):
+    service = _service_for_user(user)
+    try:
+        return service.add_lab_set_members(set_euid, payload)
+    except Exception as exc:
+        _raise_http(exc)
+    finally:
+        service.close()
+
+
 @router.get("/seq-runs/{set_euid}/samplesheet")
 async def download_seq_run_sample_sheet(
     set_euid: str,
@@ -137,6 +212,26 @@ async def download_plate_mapping_csv(
         service.close()
 
 
+@router.post("/spreadsheet-import")
+async def import_lab_action_spreadsheet(
+    file: UploadFile = File(...),
+    dry_run: bool = Query(True),
+    user: APIUser = Depends(require_write),
+):
+    service = _service_for_user(user)
+    try:
+        data = await file.read()
+        return service.import_spreadsheet(
+            filename=file.filename or "upload.xlsx",
+            data=data,
+            dry_run=dry_run,
+        )
+    except Exception as exc:
+        _raise_http(exc)
+    finally:
+        service.close()
+
+
 @router.post("/print-euids")
 async def print_euids(
     payload: PrintEuidRequest,
diff --git a/bloom_lims/domain/lab_action_spreadsheets.py b/bloom_lims/domain/lab_action_spreadsheets.py
new file mode 100644
index 0000000..e025cc9
--- /dev/null
+++ b/bloom_lims/domain/lab_action_spreadsheets.py
@@ -0,0 +1,193 @@
+"""Spreadsheet parsing helpers for Bloom lab-action uploads."""
+
+from __future__ import annotations
+
+import csv
+import io
+import re
+import zipfile
+from dataclasses import dataclass
+from pathlib import PurePosixPath
+from typing import Any
+from xml.etree import ElementTree
+
+
+@dataclass(frozen=True)
+class ParsedSheet:
+    name: str
+    headers: list[str]
+    rows: list[dict[str, Any]]
+
+
+_NS = {
+    "main": "http://schemas.openxmlformats.org/spreadsheetml/2006/main",
+    "rel": "http://schemas.openxmlformats.org/officeDocument/2006/relationships",
+    "pkgrel": "http://schemas.openxmlformats.org/package/2006/relationships",
+}
+
+
+def normalize_header(value: Any) -> str:
+    """Normalize operator spreadsheet headers to stable snake_case keys."""
+    text = str(value or "").strip().lower()
+    replacements = {
+        "continer": "container",
+        "conteiner": "container",
+        "templae": "template",
+        "destination": "target",
+        "(r)": "",
+        "(data)": "",
+    }
+    for bad, good in replacements.items():
+        text = text.replace(bad, good)
+    text = text.replace("/", " ")
+    text = re.sub(r"[^a-z0-9]+", "_", text)
+    text = re.sub(r"_+", "_", text).strip("_")
+    return text
+
+
+def _cell_column_index(cell_ref: str) -> int:
+    match = re.match(r"([A-Z]+)", cell_ref.upper())
+    if not match:
+        return 0
+    value = 0
+    for char in match.group(1):
+        value = value * 26 + (ord(char) - ord("A") + 1)
+    return value - 1
+
+
+def _xml_text(element: ElementTree.Element | None) -> str:
+    if element is None:
+        return ""
+    return "".join(element.itertext())
+
+
+def _shared_strings(archive: zipfile.ZipFile) -> list[str]:
+    try:
+        root = ElementTree.fromstring(archive.read("xl/sharedStrings.xml"))
+    except KeyError:
+        return []
+    strings: list[str] = []
+    for item in root.findall("main:si", _NS):
+        strings.append(_xml_text(item))
+    return strings
+
+
+def _sheet_paths(archive: zipfile.ZipFile) -> list[tuple[str, str]]:
+    workbook = ElementTree.fromstring(archive.read("xl/workbook.xml"))
+    rels = ElementTree.fromstring(archive.read("xl/_rels/workbook.xml.rels"))
+    rel_by_id = {
+        rel.attrib["Id"]: rel.attrib["Target"]
+        for rel in rels.findall("pkgrel:Relationship", _NS)
+    }
+    sheets: list[tuple[str, str]] = []
+    for sheet in workbook.findall("main:sheets/main:sheet", _NS):
+        rel_id = sheet.attrib.get(f"{{{_NS['rel']}}}id", "")
+        target = rel_by_id.get(rel_id)
+        if not target:
+            continue
+        clean_target = target.lstrip("/")
+        path = (
+            PurePosixPath(clean_target)
+            if clean_target.startswith("xl/")
+            else PurePosixPath("xl") / clean_target
+        )
+        sheets.append((sheet.attrib.get("name", "Sheet"), str(path)))
+    return sheets
+
+
+def _parse_xlsx_sheet(
+    archive: zipfile.ZipFile, path: str, shared_strings: list[str]
+) -> list[list[Any]]:
+    root = ElementTree.fromstring(archive.read(path))
+    rows: list[list[Any]] = []
+    for row_el in root.findall(".//main:sheetData/main:row", _NS):
+        values: list[Any] = []
+        for cell in row_el.findall("main:c", _NS):
+            col_index = _cell_column_index(cell.attrib.get("r", "A"))
+            while len(values) <= col_index:
+                values.append(None)
+            cell_type = cell.attrib.get("t")
+            value_el = cell.find("main:v", _NS)
+            if cell_type == "s":
+                raw = _xml_text(value_el)
+                values[col_index] = (
+                    shared_strings[int(raw)] if raw and raw.isdigit() else raw
+                )
+            elif cell_type == "inlineStr":
+                values[col_index] = _xml_text(cell.find("main:is", _NS))
+            else:
+                raw = _xml_text(value_el)
+                values[col_index] = raw if raw != "" else None
+        rows.append(values)
+    return rows
+
+
+def _find_header_row(rows: list[list[Any]]) -> int | None:
+    best_index = None
+    best_score = 0
+    for index, row in enumerate(rows[:20]):
+        headers = [normalize_header(value) for value in row]
+        non_empty = [header for header in headers if header]
+        score = len(set(non_empty))
+        if any(
+            token in set(non_empty)
+            for token in {
+                "tube_euid",
+                "container_euid",
+                "source_well_euid",
+                "pool_tube_euid",
+                "annotation_template_euid",
+            }
+        ):
+            score += 10
+        if score > best_score:
+            best_score = score
+            best_index = index
+    return best_index if best_score >= 2 else None
+
+
+def _rows_to_sheet(name: str, rows: list[list[Any]]) -> ParsedSheet:
+    header_index = _find_header_row(rows)
+    if header_index is None:
+        return ParsedSheet(name=name, headers=[], rows=[])
+    headers = [normalize_header(value) for value in rows[header_index]]
+    seen: dict[str, int] = {}
+    unique_headers: list[str] = []
+    for index, header in enumerate(headers):
+        if not header:
+            header = f"unnamed_{index + 1}"
+        count = seen.get(header, 0)
+        seen[header] = count + 1
+        unique_headers.append(header if count == 0 else f"{header}_{count + 1}")
+    parsed_rows: list[dict[str, Any]] = []
+    for row in rows[header_index + 1 :]:
+        item = {
+            header: row[index] if index < len(row) else None
+            for index, header in enumerate(unique_headers)
+        }
+        if any(value not in (None, "") for value in item.values()):
+            parsed_rows.append(item)
+    return ParsedSheet(name=name, headers=unique_headers, rows=parsed_rows)
+
+
+def parse_workbook(filename: str, data: bytes) -> list[ParsedSheet]:
+    """Parse CSV/XLSX data into normalized sheets.
+
+    This function intentionally avoids optional Excel dependencies so deployed
+    Bloom containers can accept simple operator workbooks without changing the
+    runtime package set.
+    """
+    suffix = filename.rsplit(".", 1)[-1].lower() if "." in filename else ""
+    if suffix == "csv":
+        text = data.decode("utf-8-sig")
+        reader = csv.reader(io.StringIO(text))
+        return [_rows_to_sheet("CSV", list(reader))]
+    if suffix != "xlsx":
+        raise ValueError("Spreadsheet upload must be .csv or .xlsx")
+    sheets: list[ParsedSheet] = []
+    with zipfile.ZipFile(io.BytesIO(data)) as archive:
+        shared_strings = _shared_strings(archive)
+        for sheet_name, sheet_path in _sheet_paths(archive):
+            rows = _parse_xlsx_sheet(archive, sheet_path, shared_strings)
+            sheets.append(_rows_to_sheet(sheet_name, rows))
+    return sheets
diff --git a/bloom_lims/domain/lab_actions.py b/bloom_lims/domain/lab_actions.py
index 6f4588c..6579bc1 100644
--- a/bloom_lims/domain/lab_actions.py
+++ b/bloom_lims/domain/lab_actions.py
@@ -5,18 +5,26 @@
 import csv
 import io
 import json
+import re
 from dataclasses import dataclass
 from typing import Any
 
 from sqlalchemy.orm.attributes import flag_modified
 
 from bloom_lims.domain.base import BloomObj
+from bloom_lims.domain.lab_action_spreadsheets import ParsedSheet, parse_workbook
 from bloom_lims.domain.v0_graph import attach_bloom_v0_edge, object_evidence
 from bloom_lims.integrations.zebra_day import ZebraDayService
 from bloom_lims.schemas.lab_actions import (
     ExtractionPlateRequest,
+    ExtractionQcAssignment,
+    ExtractionQcPlateRequest,
     ExtractionTubeAssignment,
+    LabSetMembersRequest,
+    LabSetRequest,
     LibraryPlateAssignment,
+    PlateWellDataRecord,
+    PlateWellDataRequest,
     PrintEuidRequest,
     RunSetInput,
     SeqLibraryPlateRequest,
@@ -37,6 +45,11 @@
 POOL_TUBE_TEMPLATE_CODE = "container/tube/tube-generic-10ml/1.0/"
 POOL_CONTENT_TEMPLATE_CODE = "content/pool/sequencing-library/1.0/"
 GDNA_QUANT_TEMPLATE_CODE = "data/quantification/gdna/1.0/"
+EXTRACTION_QC_TEMPLATE_CODE = "data/operation/extraction-qc/1.0/"
+
+
+def re_split_multi(value: str) -> list[str]:
+    return re.split(r"[\n,|;]+", value)
 
 
 @dataclass(frozen=True)
@@ -256,9 +269,9 @@ def _run_set(
                 "members": members,
                 "external_members": payload.external_members,
                 "metadata": payload.metadata,
-                "status": "created",
+                "status": payload.status,
             },
-            status="created",
+            status=payload.status,
         )
         for member in members:
             if self.bobj.get_by_euid(member) is None:
@@ -267,6 +280,233 @@ def _run_set(
             self._create_lineage(member, instance.euid, "associated_set")
         return instance
 
+    def _well_from_plate_position(self, plate_euid: str, row: str, col: int):
+        plate = self._require(plate_euid)
+        wells = self._plate_wells(plate)
+        position = WellPosition(row=row, col=col).name
+        well = wells.get(position)
+        if well is None:
+            raise ValueError(f"Destination well not found on plate: {position}")
+        return well
+
+    def _well_for_data_record(self, record: PlateWellDataRecord):
+        if record.well_euid:
+            return self._require(record.well_euid)
+        return self._well_from_plate_position(record.plate_euid, record.row, record.col)
+
+    def _well_for_qc_assignment(
+        self, assignment: ExtractionQcAssignment, source_plate_euid: str | None
+    ):
+        if assignment.source_well_euid:
+            return self._require(assignment.source_well_euid)
+        if not source_plate_euid:
+            raise ValueError("source_plate_euid is required when assignment uses row/col")
+        return self._well_from_plate_position(
+            source_plate_euid, assignment.row, assignment.col
+        )
+
+    def _create_or_get_qc_plate(self, request: ExtractionQcPlateRequest):
+        if request.qc_plate_euid:
+            plate = self._require(request.qc_plate_euid)
+            if instance_semantic_category(plate) != "container" or plate.type != "plate":
+                raise ValueError(f"{request.qc_plate_euid} is not a plate container")
+            return plate, []
+        plate = self._create_by_code(
+            EXTRACTION_PLATE_TEMPLATE_CODE,
+            name=request.qc_plate_name or "extraction QC plate",
+        )
+        return plate, [plate.euid]
+
+    def _all_filled_well_qc_assignments(
+        self, source_plate_euid: str
+    ) -> list[ExtractionQcAssignment]:
+        plate = self._require(source_plate_euid)
+        assignments: list[ExtractionQcAssignment] = []
+        for name, well in sorted(self._plate_wells(plate).items()):
+            if self._lineages_from_parent(well, "HOLDS_MATERIAL"):
+                assignments.append(
+                    ExtractionQcAssignment(
+                        source_well_euid=well.euid,
+                        qc_row=name[:1],
+                        qc_col=int(name[1:]),
+                    )
+                )
+        if not assignments:
+            raise ValueError(f"Source plate {source_plate_euid} has no filled wells")
+        return assignments
+
+    def create_lab_set(self, request: LabSetRequest) -> dict[str, Any]:
+        run_set = self._create_by_code(
+            RUN_SET_TEMPLATE_CODE,
+            name=request.name,
+            properties={
+                "name": request.name,
+                "description": request.description or "",
+                "members": list(dict.fromkeys(request.members)),
+                "external_members": list(dict.fromkeys(request.external_members)),
+                "operator": request.operator or "",
+                "instrument": request.instrument or "",
+                "reagents": request.reagents,
+                "machine": request.machine or "",
+                "flowcell_barcode": request.flowcell_barcode or "",
+                "status": request.status,
+                "metadata": request.metadata,
+            },
+            status=request.status,
+        )
+        for member in dict.fromkeys(request.members):
+            if self.bobj.get_by_euid(member) is not None:
+                self._create_lineage(run_set.euid, member, "run_set_member")
+                self._create_lineage(member, run_set.euid, "associated_set")
+        self.bdb.session.commit()
+        return self.get_lab_set(run_set.euid)
+
+    def add_lab_set_members(
+        self, set_euid: str, request: LabSetMembersRequest
+    ) -> dict[str, Any]:
+        run_set = self._require(set_euid)
+        props = self._props(run_set)
+        members = list(
+            dict.fromkeys([*props.get("members", []), *request.members])
+        )
+        external_members = list(
+            dict.fromkeys(
+                [*props.get("external_members", []), *request.external_members]
+            )
+        )
+        props["members"] = members
+        props["external_members"] = external_members
+        self._write_props(run_set, props)
+        for member in request.members:
+            if self.bobj.get_by_euid(member) is not None:
+                self._create_lineage(run_set.euid, member, "run_set_member")
+                self._create_lineage(member, run_set.euid, "associated_set")
+        self.bdb.session.commit()
+        return self.get_lab_set(set_euid)
+
+    def get_lab_set(self, set_euid: str) -> dict[str, Any]:
+        run_set = self._require(set_euid)
+        props = self._props(run_set)
+        return {
+            "set_euid": run_set.euid,
+            "name": run_set.name,
+            "status": run_set.bstatus,
+            "properties": props,
+            "members": props.get("members", []),
+            "external_members": props.get("external_members", []),
+        }
+
+    def fill_extraction_qc_plate(
+        self, request: ExtractionQcPlateRequest
+    ) -> dict[str, Any]:
+        assignments = request.assignments or self._all_filled_well_qc_assignments(
+            request.source_plate_euid
+        )
+        if len(assignments) > 96:
+            raise ValueError("extraction QC plate can accept at most 96 assignments")
+        qc_plate, new_container_euids = self._create_or_get_qc_plate(request)
+        qc_wells = self._plate_wells(qc_plate)
+        used_qc_positions: set[str] = set()
+        mappings: list[dict[str, Any]] = []
+        for index, assignment in enumerate(assignments):
+            source_well = self._well_for_qc_assignment(
+                assignment, request.source_plate_euid
+            )
+            source_content = self._well_content(source_well)
+            if assignment.qc_row is not None and assignment.qc_col is not None:
+                qc_position = WellPosition(
+                    row=assignment.qc_row, col=assignment.qc_col
+                ).name
+            else:
+                qc_position = WellPosition(
+                    row=assignment.row or ROWS[index // 12],
+                    col=assignment.col or (index % 12) + 1,
+                ).name
+            if qc_position in used_qc_positions:
+                raise ValueError(f"duplicate QC destination well: {qc_position}")
+            used_qc_positions.add(qc_position)
+            qc_well = qc_wells.get(qc_position)
+            if qc_well is None:
+                raise ValueError(f"QC well not found on plate: {qc_position}")
+            data = self._create_by_code(
+                EXTRACTION_QC_TEMPLATE_CODE,
+                name=f"{source_well.euid} extraction QC",
+                properties={
+                    "source_well_euid": source_well.euid,
+                    "source_content_euid": source_content.euid,
+                    "qc_plate_euid": qc_plate.euid,
+                    "qc_well_euid": qc_well.euid,
+                    "qc_well_name": qc_position,
+                    "result": assignment.result or "",
+                    "status": assignment.status or "recorded",
+                    "data": assignment.data,
+                },
+                status=assignment.status or "recorded",
+            )
+            self._create_lineage(source_well.euid, qc_well.euid, "qc_source_well")
+            self._create_lineage(qc_well.euid, data.euid, "well_associated_data")
+            self._create_lineage(source_content.euid, data.euid, "qc_for_material")
+            mappings.append(
+                {
+                    "source_well_euid": source_well.euid,
+                    "source_content_euid": source_content.euid,
+                    "qc_well_euid": qc_well.euid,
+                    "qc_well_name": qc_position,
+                    "data_euid": data.euid,
+                    "result": assignment.result or "",
+                    "status": assignment.status or "recorded",
+                }
+            )
+        run_set = self._run_set(
+            requested=request.create_run_set,
+            run_set=request.run_set,
+            default_name=f"{qc_plate.euid} extraction QC set",
+            member_euids=[qc_plate.euid, *[item["data_euid"] for item in mappings]],
+        )
+        self.bdb.session.commit()
+        return {
+            "qc_plate_euid": qc_plate.euid,
+            "run_set_euid": run_set.euid if run_set is not None else None,
+            "new_container_euids": new_container_euids,
+            "mappings": mappings,
+        }
+
+    def attach_plate_well_data(self, request: PlateWellDataRequest) -> dict[str, Any]:
+        mappings: list[dict[str, Any]] = []
+        for record in request.records:
+            well = self._well_for_data_record(record)
+            target = well if record.target == "well" else self._well_content(well)
+            data = self._create_by_code(
+                request.data_template_code,
+                name=record.name or f"{well.euid} associated data",
+                properties={
+                    "well_euid": well.euid,
+                    "target_euid": target.euid,
+                    "target_kind": record.target,
+                    "data": record.data,
+                },
+            )
+            self._create_lineage(target.euid, data.euid, request.relationship_type)
+            mappings.append(
+                {
+                    "well_euid": well.euid,
+                    "target_euid": target.euid,
+                    "data_euid": data.euid,
+                    "relationship_type": request.relationship_type,
+                }
+            )
+        run_set = self._run_set(
+            requested=request.create_run_set,
+            run_set=request.run_set,
+            default_name="plate well data set",
+            member_euids=[item["data_euid"] for item in mappings],
+        )
+        self.bdb.session.commit()
+        return {
+            "run_set_euid": run_set.euid if run_set is not None else None,
+            "mappings": mappings,
+        }
+
     def create_extraction_plate(self, request: ExtractionPlateRequest) -> dict[str, Any]:
         assignments = self._normalize_assignments(request)
         plate = self._create_or_get_extraction_plate(request)
@@ -689,6 +929,325 @@ def illumina_sample_sheet(self, set_euid: str) -> str:
         writer.writerows(data_rows)
         return output.getvalue()
 
+    def _split_values(self, value: Any) -> list[str]:
+        if value in (None, ""):
+            return []
+        return [
+            token.strip()
+            for token in re_split_multi(str(value))
+            if token and token.strip()
+        ]
+
+    def _row_metadata(self, row: dict[str, Any], *prefixes: str) -> dict[str, Any]:
+        metadata: dict[str, Any] = {}
+        for key, value in row.items():
+            if value in (None, ""):
+                continue
+            for prefix in prefixes:
+                if key.startswith(prefix):
+                    metadata[key.removeprefix(prefix)] = value
+        return metadata
+
+    def _sheet_action(self, sheet: ParsedSheet) -> str:
+        name = sheet.name.strip().lower().replace("-", " ").replace("_", " ")
+        headers = set(sheet.headers)
+        if name == "csv":
+            if {"pool_tube_euid", "flowcell_barcode"} & headers:
+                return "seq_run_set"
+            if {"input_euid", "input_euids"} & headers:
+                return "seq_pool"
+            if "source_well_euid" in headers and {"index_barcode", "index_euid"} & headers:
+                return "seq_library_plate"
+            if {"source_well_euid", "qc_row", "qc_col"} & headers:
+                return "extraction_qc"
+            if {"well_euid", "data_template_code"} & headers:
+                return "plate_well_data"
+            if {"set_name", "members", "member_euids"} & headers:
+                return "sets"
+            if "tube_euid" in headers:
+                return "extraction_plate"
+        if name in {"extraction plate", "extraction"}:
+            return "extraction_plate"
+        if name in {"extraction qc", "extractionqc", "extraction qc plate"}:
+            return "extraction_qc"
+        if name in {"seq library plate", "sequencing library plate", "library plate"}:
+            return "seq_library_plate"
+        if name in {"seq pool", "sequencing pool", "seq library pool", "pool"}:
+            return "seq_pool"
+        if name in {"seq run", "seq run set", "sequencing run", "sequencing run set"}:
+            return "seq_run_set"
+        if name in {"sets", "set", "run sets", "run set"}:
+            return "sets"
+        if name in {"plate well data", "well data", "annotation"}:
+            return "plate_well_data" if name != "annotation" else "container_annotation_preview"
+        if name in {"bulk create", "transfer"}:
+            return "container_interaction_preview"
+        return "unknown"
+
+    def _request_from_extraction_sheet(self, sheet: ParsedSheet) -> ExtractionPlateRequest:
+        assignments: list[ExtractionTubeAssignment] = []
+        tube_euids: list[str] = []
+        plate_name: str | None = None
+        for row in sheet.rows:
+            tube_euid = str(
+                row.get("tube_euid") or row.get("container_euid") or ""
+            ).strip()
+            if not tube_euid:
+                continue
+            plate_name = plate_name or str(row.get("plate_name") or "").strip() or None
+            row_name = row.get("row") or row.get("well_row") or row.get("child_container_row")
+            col_value = row.get("col") or row.get("well_col") or row.get("child_container_column")
+            if row_name not in (None, "") or col_value not in (None, ""):
+                assignments.append(
+                    ExtractionTubeAssignment(
+                        tube_euid=tube_euid,
+                        row=row_name,
+                        col=col_value,
+                        quant=self._row_metadata(row, "quant_", "qc_"),
+                    )
+                )
+            else:
+                tube_euids.append(tube_euid)
+        if assignments:
+            return ExtractionPlateRequest(
+                mode="directed",
+                assignments=assignments,
+                plate_name=plate_name or "extraction plate",
+            )
+        return ExtractionPlateRequest(
+            mode="auto",
+            tube_euids=tube_euids,
+            plate_name=plate_name or "extraction plate",
+        )
+
+    def _request_from_qc_sheet(self, sheet: ParsedSheet) -> ExtractionQcPlateRequest:
+        source_plate_euid = None
+        qc_plate_name = None
+        assignments: list[ExtractionQcAssignment] = []
+        for row in sheet.rows:
+            source_plate_euid = source_plate_euid or str(
+                row.get("source_plate_euid") or row.get("plate_euid") or ""
+            ).strip() or None
+            qc_plate_name = qc_plate_name or str(row.get("qc_plate_name") or "").strip() or None
+            assignments.append(
+                ExtractionQcAssignment(
+                    source_well_euid=str(row.get("source_well_euid") or row.get("well_euid") or "").strip()
+                    or None,
+                    row=row.get("row") or row.get("well_row"),
+                    col=row.get("col") or row.get("well_col"),
+                    qc_row=row.get("qc_row") or row.get("target_row"),
+                    qc_col=row.get("qc_col") or row.get("target_col"),
+                    result=str(row.get("result") or "").strip() or None,
+                    status=str(row.get("status") or "").strip() or None,
+                    data=self._row_metadata(row, "data_", "qc_", "metric_"),
+                )
+            )
+        return ExtractionQcPlateRequest(
+            source_plate_euid=source_plate_euid,
+            qc_plate_name=qc_plate_name or "extraction QC plate",
+            assignments=assignments,
+        )
+
+    def _request_from_library_sheet(self, sheet: ParsedSheet) -> SeqLibraryPlateRequest:
+        source_plate_euid = None
+        plate_name = None
+        assignments: list[LibraryPlateAssignment] = []
+        for row in sheet.rows:
+            source_plate_euid = source_plate_euid or str(
+                row.get("source_plate_euid") or ""
+            ).strip() or None
+            plate_name = plate_name or str(row.get("plate_name") or "").strip() or None
+            source_well_euid = str(row.get("source_well_euid") or row.get("well_euid") or "").strip()
+            if source_well_euid:
+                assignments.append(
+                    LibraryPlateAssignment(
+                        source_well_euid=source_well_euid,
+                        row=row.get("row") or row.get("well_row"),
+                        col=row.get("col") or row.get("well_col"),
+                        index_barcode=str(row.get("index_barcode") or "").strip() or None,
+                        index_euid=str(row.get("index_euid") or "").strip() or None,
+                        data=self._row_metadata(row, "data_", "library_"),
+                    )
+                )
+        if assignments:
+            return SeqLibraryPlateRequest(
+                mode="directed",
+                assignments=assignments,
+                plate_name=plate_name or "seq library plate",
+            )
+        return SeqLibraryPlateRequest(
+            mode="plate_1_to_1",
+            source_plate_euid=source_plate_euid,
+            plate_name=plate_name or "seq library plate",
+        )
+
+    def _request_from_pool_sheet(self, sheet: ParsedSheet) -> SeqLibraryPoolRequest:
+        input_euids: list[str] = []
+        platform = "ILMN"
+        pool_tube_euid = None
+        pool_name = None
+        metadata: dict[str, Any] = {}
+        for row in sheet.rows:
+            input_euids.extend(
+                self._split_values(
+                    row.get("input_euid")
+                    or row.get("input_euids")
+                    or row.get("well_euid")
+                    or row.get("tube_euid")
+                    or row.get("container_euid")
+                    or row.get("content_euid")
+                )
+            )
+            platform = str(row.get("platform") or platform).strip() or platform
+            pool_tube_euid = pool_tube_euid or str(row.get("pool_tube_euid") or "").strip() or None
+            pool_name = pool_name or str(row.get("pool_name") or "").strip() or None
+            metadata.update(self._row_metadata(row, "metadata_", "pool_"))
+        return SeqLibraryPoolRequest(
+            input_euids=list(dict.fromkeys(input_euids)),
+            platform=platform,
+            pool_tube_euid=pool_tube_euid,
+            pool_name=pool_name or "seq library",
+            metadata=metadata,
+        )
+
+    def _request_from_run_sheet(self, sheet: ParsedSheet) -> SeqRunSetRequest:
+        if not sheet.rows:
+            raise ValueError("Seq Run Set sheet has no rows")
+        row = sheet.rows[0]
+        return SeqRunSetRequest(
+            pool_tube_euid=str(row.get("pool_tube_euid") or "").strip(),
+            pool_content_euid=str(row.get("pool_content_euid") or "").strip() or None,
+            platform=str(row.get("platform") or "ILMN").strip() or "ILMN",
+            operator=str(row.get("operator") or "").strip() or None,
+            instrument_euid=str(row.get("instrument_euid") or "").strip() or None,
+            machine=str(row.get("machine") or "").strip() or None,
+            flowcell_barcode=str(row.get("flowcell_barcode") or row.get("flowcell") or "").strip(),
+            reagent_euids=self._split_values(row.get("reagent_euids") or row.get("reagents")),
+            status=str(row.get("status") or "created").strip() or "created",
+            name=str(row.get("name") or "").strip() or None,
+            description=str(row.get("description") or "").strip() or None,
+            metadata=self._row_metadata(row, "metadata_", "run_"),
+        )
+
+    def _request_from_data_sheet(self, sheet: ParsedSheet) -> PlateWellDataRequest:
+        records: list[PlateWellDataRecord] = []
+        data_template_code = "data/operation/extraction-qc/1.0/"
+        relationship_type = "well_associated_data"
+        for row in sheet.rows:
+            data_template_code = str(
+                row.get("data_template_code")
+                or row.get("annotation_template_euid")
+                or data_template_code
+            ).strip()
+            relationship_type = str(row.get("relationship_type") or relationship_type).strip()
+            records.append(
+                PlateWellDataRecord(
+                    well_euid=str(row.get("well_euid") or row.get("child_container_euid") or "").strip()
+                    or None,
+                    plate_euid=str(row.get("plate_euid") or row.get("container_euid") or "").strip()
+                    or None,
+                    row=row.get("row") or row.get("well_row") or row.get("child_container_row"),
+                    col=row.get("col") or row.get("well_col") or row.get("child_container_column"),
+                    name=str(row.get("name") or row.get("annotation_name") or "").strip()
+                    or None,
+                    target="content"
+                    if "content"
+                    in str(
+                        row.get("target")
+                        or row.get("annotate_container_child_container_content")
+                        or "content"
+                    ).strip().lower()
+                    else "well",
+                    data={
+                        **self._row_metadata(row, "data_", "annotation_", "metric_"),
+                        **({"value": row.get("annotation_value")} if row.get("annotation_value") not in (None, "") else {}),
+                    },
+                )
+            )
+        return PlateWellDataRequest(
+            data_template_code=data_template_code,
+            relationship_type=relationship_type,
+            records=records,
+        )
+
+    def _requests_from_sets_sheet(self, sheet: ParsedSheet) -> list[LabSetRequest]:
+        requests: list[LabSetRequest] = []
+        for row in sheet.rows:
+            name = str(row.get("name") or row.get("set_name") or "").strip()
+            if not name:
+                continue
+            requests.append(
+                LabSetRequest(
+                    name=name,
+                    description=str(row.get("description") or "").strip() or None,
+                    members=self._split_values(row.get("members") or row.get("member_euids")),
+                    external_members=self._split_values(row.get("external_members")),
+                    operator=str(row.get("operator") or "").strip() or None,
+                    instrument=str(row.get("instrument") or row.get("instrument_euid") or "").strip() or None,
+                    reagents=self._split_values(row.get("reagents") or row.get("reagent_euids")),
+                    machine=str(row.get("machine") or "").strip() or None,
+                    flowcell_barcode=str(row.get("flowcell_barcode") or "").strip() or None,
+                    status=str(row.get("status") or "created").strip() or "created",
+                    metadata=self._row_metadata(row, "metadata_", "set_"),
+                )
+            )
+        return requests
+
+    def import_spreadsheet(
+        self, *, filename: str, data: bytes, dry_run: bool = True
+    ) -> dict[str, Any]:
+        sheets = parse_workbook(filename, data)
+        actions: list[dict[str, Any]] = []
+        for sheet in sheets:
+            action = self._sheet_action(sheet)
+            entry: dict[str, Any] = {
+                "sheet": sheet.name,
+                "action": action,
+                "headers": sheet.headers,
+                "row_count": len(sheet.rows),
+            }
+            if action in {"container_interaction_preview", "container_annotation_preview", "unknown"}:
+                entry["preview_rows"] = sheet.rows[:25]
+                actions.append(entry)
+                continue
+            if action == "extraction_plate":
+                request = self._request_from_extraction_sheet(sheet)
+                entry["request"] = request.model_dump(mode="json")
+                if not dry_run:
+                    entry["result"] = self.create_extraction_plate(request)
+            elif action == "extraction_qc":
+                request = self._request_from_qc_sheet(sheet)
+                entry["request"] = request.model_dump(mode="json")
+                if not dry_run:
+                    entry["result"] = self.fill_extraction_qc_plate(request)
+            elif action == "seq_library_plate":
+                request = self._request_from_library_sheet(sheet)
+                entry["request"] = request.model_dump(mode="json")
+                if not dry_run:
+                    entry["result"] = self.create_seq_library_plate(request)
+            elif action == "seq_pool":
+                request = self._request_from_pool_sheet(sheet)
+                entry["request"] = request.model_dump(mode="json")
+                if not dry_run:
+                    entry["result"] = self.create_seq_library_pool(request)
+            elif action == "seq_run_set":
+                request = self._request_from_run_sheet(sheet)
+                entry["request"] = request.model_dump(mode="json")
+                if not dry_run:
+                    entry["result"] = self.create_seq_run_set(request)
+            elif action == "plate_well_data":
+                request = self._request_from_data_sheet(sheet)
+                entry["request"] = request.model_dump(mode="json")
+                if not dry_run:
+                    entry["result"] = self.attach_plate_well_data(request)
+            elif action == "sets":
+                requests = self._requests_from_sets_sheet(sheet)
+                entry["request"] = [item.model_dump(mode="json") for item in requests]
+                if not dry_run:
+                    entry["result"] = [self.create_lab_set(item) for item in requests]
+            actions.append(entry)
+        return {"filename": filename, "dry_run": dry_run, "actions": actions}
+
     def print_euids(self, request: PrintEuidRequest) -> dict[str, Any]:
         service = ZebraDayService()
         results = []
diff --git a/bloom_lims/schemas/lab_actions.py b/bloom_lims/schemas/lab_actions.py
index 6900f07..73c281c 100644
--- a/bloom_lims/schemas/lab_actions.py
+++ b/bloom_lims/schemas/lab_actions.py
@@ -56,6 +56,7 @@ class RunSetInput(BaseModel):
     members: list[str] = Field(default_factory=list)
     external_members: list[str] = Field(default_factory=list)
     metadata: dict[str, Any] = Field(default_factory=dict)
+    status: RunSetStatus = "created"
 
 
 class ExtractionPlateRequest(BaseModel):
@@ -118,6 +119,83 @@ def validate_input(self) -> "SeqLibraryPlateRequest":
         return self
 
 
+class ExtractionQcAssignment(BaseModel):
+    source_well_euid: str | None = None
+    row: str | None = None
+    col: int | None = None
+    qc_row: str | None = None
+    qc_col: int | None = None
+    result: str | None = None
+    status: str | None = None
+    data: dict[str, Any] = Field(default_factory=dict)
+
+    @model_validator(mode="after")
+    def validate_source_position(self) -> "ExtractionQcAssignment":
+        if self.source_well_euid and (self.row is not None or self.col is not None):
+            raise ValueError("provide source_well_euid or row/col, not both")
+        if not self.source_well_euid and (self.row is None or self.col is None):
+            raise ValueError("source_well_euid or row/col is required")
+        if (self.row is None) ^ (self.col is None):
+            raise ValueError("row and col must be provided together")
+        if self.row is not None and self.col is not None:
+            WellPosition(row=self.row, col=self.col)
+        if (self.qc_row is None) ^ (self.qc_col is None):
+            raise ValueError("qc_row and qc_col must be provided together")
+        if self.qc_row is not None and self.qc_col is not None:
+            WellPosition(row=self.qc_row, col=self.qc_col)
+        return self
+
+
+class ExtractionQcPlateRequest(BaseModel):
+    source_plate_euid: str | None = None
+    qc_plate_euid: str | None = None
+    qc_plate_name: str | None = None
+    assignments: list[ExtractionQcAssignment] = Field(default_factory=list)
+    create_run_set: bool = False
+    run_set: RunSetInput | None = None
+
+    @model_validator(mode="after")
+    def validate_input(self) -> "ExtractionQcPlateRequest":
+        if not self.source_plate_euid and not self.assignments:
+            raise ValueError("source_plate_euid or assignments is required")
+        return self
+
+
+class PlateWellDataRecord(BaseModel):
+    well_euid: str | None = None
+    plate_euid: str | None = None
+    row: str | None = None
+    col: int | None = None
+    name: str | None = None
+    target: Literal["well", "content"] = "content"
+    data: dict[str, Any] = Field(default_factory=dict)
+
+    @model_validator(mode="after")
+    def validate_target(self) -> "PlateWellDataRecord":
+        if self.well_euid and (self.plate_euid or self.row is not None or self.col is not None):
+            raise ValueError("provide well_euid or plate_euid with row/col, not both")
+        if not self.well_euid:
+            if not self.plate_euid or self.row is None or self.col is None:
+                raise ValueError("well_euid or plate_euid with row/col is required")
+            WellPosition(row=self.row, col=self.col)
+        return self
+
+
+class PlateWellDataRequest(BaseModel):
+    data_template_code: str = "data/operation/extraction-qc/1.0/"
+    relationship_type: str = "well_associated_data"
+    records: list[PlateWellDataRecord]
+    create_run_set: bool = False
+    run_set: RunSetInput | None = None
+
+    @field_validator("records")
+    @classmethod
+    def validate_records(cls, value):
+        if not value:
+            raise ValueError("records must not be empty")
+        return value
+
+
 class SeqLibraryPoolRequest(BaseModel):
     input_euids: list[str]
     platform: PlatformName = "ILMN"
@@ -151,6 +229,31 @@ class SeqRunSetRequest(BaseModel):
     metadata: dict[str, Any] = Field(default_factory=dict)
 
 
+class LabSetRequest(BaseModel):
+    name: str
+    description: str | None = None
+    members: list[str] = Field(default_factory=list)
+    external_members: list[str] = Field(default_factory=list)
+    operator: str | None = None
+    instrument: str | None = None
+    reagents: list[str] = Field(default_factory=list)
+    machine: str | None = None
+    flowcell_barcode: str | None = None
+    status: RunSetStatus = "created"
+    metadata: dict[str, Any] = Field(default_factory=dict)
+
+
+class LabSetMembersRequest(BaseModel):
+    members: list[str] = Field(default_factory=list)
+    external_members: list[str] = Field(default_factory=list)
+
+    @model_validator(mode="after")
+    def validate_members(self) -> "LabSetMembersRequest":
+        if not self.members and not self.external_members:
+            raise ValueError("members or external_members is required")
+        return self
+
+
 class PrintEuidRequest(BaseModel):
     euids: list[str]
     lab: str
diff --git a/docs/apis.md b/docs/apis.md
index 55e89d5..f283ea6 100644
--- a/docs/apis.md
+++ b/docs/apis.md
@@ -370,9 +370,15 @@ The detailed operator/API runbook is [`lab_actions.md`](lab_actions.md). It is t
 Current routes:
 
 - `POST /api/v1/lab-actions/extraction-plates`: create or fill extraction plates from incoming filled tube EUIDs, create gDNA contents, and link tube/content/well/material provenance.
+- `POST /api/v1/lab-actions/extraction-qc-plates`: create or fill extraction QC plates from extraction wells and attach QC data records.
 - `POST /api/v1/lab-actions/seq-library-plates`: create sequencing-library plates from filled extraction wells or directed mappings.
 - `POST /api/v1/lab-actions/seq-library-pools`: create or fill sequencing-library pool tubes from tube, well, content, or existing pool inputs.
 - `POST /api/v1/lab-actions/seq-runs`: create sequencing run sets with pool, instrument/operator/reagent metadata, flowcell barcode, platform, and status.
+- `POST /api/v1/lab-actions/sets`: create generic lab/run sets for batches, reagents, instruments, operators, or external members.
+- `GET /api/v1/lab-actions/sets/{set_euid}`: read the stored set metadata and members.
+- `POST /api/v1/lab-actions/sets/{set_euid}/members`: append internal Bloom EUID members or external member identifiers.
+- `POST /api/v1/lab-actions/plate-well-data`: attach structured data records to plate wells or well contents.
+- `POST /api/v1/lab-actions/spreadsheet-import`: dry-run or execute `.csv`/`.xlsx` uploads for explicit lab-action sheet shapes.
 - `GET /api/v1/lab-actions/seq-runs/{set_euid}/samplesheet`: download ILMN sample sheets. Non-ILMN platforms fail explicitly until file formats are specified.
 - `GET /api/v1/lab-actions/plates/{plate_euid}/mapping.csv`: export one-degree parent/child plate mapping CSV.
 - `POST /api/v1/lab-actions/print-euids`: dispatch EUID barcode print requests through Zebra Day.
diff --git a/docs/gui.md b/docs/gui.md
index b0ebee2..e4be089 100644
--- a/docs/gui.md
+++ b/docs/gui.md
@@ -207,9 +207,13 @@ Older workflow/workset-centric creation surfaces are not the current product dir
 `/lab-actions` exposes the temporary wet-lab action wizard for:
 
 - incoming tube to extraction plate mapping
+- extraction plate to extraction QC plate mapping
 - extraction plate to sequencing-library plate mapping
 - sequencing-library pool tube creation
 - sequencing run set setup
+- generic lab/run set creation and member management
+- plate-well associated data attachment
+- spreadsheet upload for `.csv` and `.xlsx` lab-action sheets
 - plate CSV export
 - ILMN sample-sheet download
 - generic EUID barcode print dispatch
diff --git a/docs/lab_actions.md b/docs/lab_actions.md
index 21ec10a..3b5ec61 100644
--- a/docs/lab_actions.md
+++ b/docs/lab_actions.md
@@ -89,7 +89,34 @@ Directed mode lets the caller specify destination wells. It can create a new pla
 
 The action creates gDNA content in each destination well, links the tube to the well, and links the incoming tube content to the new gDNA content.
 
-### 2. Sequencing-Library Plate
+### 2. Extraction QC Plate
+
+Extraction QC fills a new or existing QC plate from an extraction plate. If assignments are omitted, Bloom uses every filled source well from the source extraction plate in row-major order. Explicit assignments can name source wells, destination QC wells, result/status, and structured QC data.
+
+```bash
+curl -sS -X POST "$BLOOM_URL/api/v1/lab-actions/extraction-qc-plates" \
+  -H "Authorization: Bearer $BLOOM_TOKEN" \
+  -H "Content-Type: application/json" \
+  -d '{
+    "source_plate_euid": "Z-BCP-EXTRACTION",
+    "qc_plate_name": "extraction QC plate",
+    "assignments": [
+      {
+        "source_well_euid": "Z-BCW-SOURCEA1",
+        "qc_row": "A",
+        "qc_col": 1,
+        "result": "pass",
+        "status": "recorded",
+        "data": {"concentration_ng_ul": 43.2, "a260_280": 1.83}
+      }
+    ],
+    "create_run_set": true
+  }'
+```
+
+The action creates `data/operation/extraction-qc/1.0/` records, links source well/content to QC well/data, and rejects requests above the 96-well plate capacity.
+
+### 3. Sequencing-Library Plate
 
 `plate_1_to_1` mode maps every filled extraction well to the same position on a new sequencing-library plate.
 
@@ -106,7 +133,7 @@ curl -sS -X POST "$BLOOM_URL/api/v1/lab-actions/seq-library-plates" \
 
 Directed mode accepts explicit input wells and output wells. Optional fields include `index_barcode`, `index_euid`, and arbitrary per-well `data`.
 
-### 3. Sequencing-Library Pool Tube
+### 4. Sequencing-Library Pool Tube
 
 Pools accept input tube EUIDs, well EUIDs, content EUIDs, or existing pool EUIDs. The action creates or fills a pool tube and creates sequencing-library pool content.
 
@@ -123,7 +150,58 @@ curl -sS -X POST "$BLOOM_URL/api/v1/lab-actions/seq-library-pools" \
 
 Supported platform metadata values are `ILMN`, `ONT`, `Ultima`, `PacBio`, and `CompleteGenomics`.
 
-### 4. Sequencing Run Set
+### 5. Generic Lab Sets
+
+Sets use the `set/run-set/generic/1.01` template for lightweight batch/run grouping. They can hold Bloom EUID members, external EUID/string members, operator/instrument/reagent metadata, status, and arbitrary metadata. Set membership is modeled with lineage and stored properties; it does not drive queues or execution.
+
+```bash
+curl -sS -X POST "$BLOOM_URL/api/v1/lab-actions/sets" \
+  -H "Authorization: Bearer $BLOOM_TOKEN" \
+  -H "Content-Type: application/json" \
+  -d '{
+    "name": "extraction reagent set",
+    "description": "Reagents, machine, and operator for extraction batch",
+    "members": ["Z-BEQ-INSTRUMENT"],
+    "external_members": ["lot:REAGENT-2026-06-18"],
+    "operator": "operator@example.com",
+    "status": "created",
+    "metadata": {"bench": "SSF"}
+  }'
+```
+
+Members can be appended later:
+
+```bash
+curl -sS -X POST "$BLOOM_URL/api/v1/lab-actions/sets/Z-BGS-SET/members" \
+  -H "Authorization: Bearer $BLOOM_TOKEN" \
+  -H "Content-Type: application/json" \
+  -d '{"members": ["Z-BCT-TUBE"], "external_members": ["vendor-kit:123"]}'
+```
+
+### 6. Plate-Well Associated Data
+
+Per-well data can be attached to a well or the well content. This is intentionally generic so operators can capture QC, quantification, or other measurements without introducing a new workflow engine.
+
+```bash
+curl -sS -X POST "$BLOOM_URL/api/v1/lab-actions/plate-well-data" \
+  -H "Authorization: Bearer $BLOOM_TOKEN" \
+  -H "Content-Type: application/json" \
+  -d '{
+    "plate_euid": "Z-BCP-EXTRACTION",
+    "records": [
+      {
+        "row": "A",
+        "col": 1,
+        "data_template_code": "data/quantification/gdna/1.0/",
+        "name": "A1 gDNA quant",
+        "target": "content",
+        "data": {"concentration_ng_ul": 43.2}
+      }
+    ]
+  }'
+```
+
+### 7. Sequencing Run Set
 
 Sequencing run setup creates a `set/run-set/generic/1.01` object with pool, operator, instrument, reagent, flowcell, status, and platform metadata.
 
@@ -160,6 +238,32 @@ The sample sheet includes the run-set EUID and library mappings so OWY can walk
 
 Non-ILMN sample-sheet downloads fail explicitly until concrete file formats are specified. There is no fallback manifest.
 
+### Spreadsheet Uploads
+
+Spreadsheet uploads are available at:
+
+```bash
+curl -sS -X POST "$BLOOM_URL/api/v1/lab-actions/spreadsheet-import?dry_run=true" \
+  -H "Authorization: Bearer $BLOOM_TOKEN" \
+  -F "file=@lab-actions.xlsx"
+```
+
+Use `dry_run=false` to execute supported sheets after previewing the parsed operations. The parser accepts `.xlsx` and `.csv`; other extensions fail explicitly. The parser normalizes common operator header typos such as `Continer`, `Conteiner`, and `Templae`.
+
+Executable sheet names:
+
+| Sheet | Purpose | Key columns |
+|---|---|---|
+| `Extraction Plate` | Create or fill extraction plate from incoming tubes. | `tube_euid`, `row`, `col`, `plate_euid`, `plate_name`, `run_set_name`, `print_labels` |
+| `Extraction QC` | Fill extraction QC plate from extraction wells. | `source_plate_euid`, `source_well_euid`, `source_row`, `source_col`, `qc_plate_euid`, `qc_plate_name`, `qc_row`, `qc_col`, `result`, `status`, `data` |
+| `Seq Library Plate` | Create library plate from extraction wells. | `source_plate_euid`, `source_well_euid`, `source_row`, `source_col`, `output_row`, `output_col`, `index_barcode`, `index_euid`, `data` |
+| `Seq Pool` | Create/fill pool tube from wells, tubes, contents, or pools. | `input_euids`, `pool_tube_euid`, `pool_name`, `pool_content_name`, `platform`, `run_set_name`, `print_labels` |
+| `Seq Run Set` | Create sequencing run set from a pool and run metadata. | `pool_tube_euid`, `pool_content_euid`, `platform`, `operator`, `instrument_euid`, `flowcell_barcode`, `reagent_euids`, `status`, `metadata` |
+| `Sets` | Create generic sets. | `name`, `description`, `members`, `external_members`, `operator`, `instrument`, `reagents`, `machine`, `flowcell_barcode`, `status`, `metadata` |
+| `Plate Well Data` | Attach data records to wells or contents. | `plate_euid`, `well_euid`, `row`, `col`, `target`, `data_template_code`, `name`, `data` |
+
+The example workbook family with `Bulk Create`, `Transfer`, and `Annotation` sheets is parsed and previewed as container-interaction evidence. Those sheets are not blindly executed because they can describe broad generic operations; executable lab-action sheets use the specific names above.
+
 ### Plate Mapping CSV
 
 Any plate-like container can export a one-degree mapping CSV:
@@ -209,14 +313,19 @@ Recursive templates, such as 96-well plates, reject `count > 1` because a single
 
 Open `/lab-actions`.
 
-The wizard has four panels:
+The wizard has these panels:
 
 1. Extraction Plate.
-2. Sequencing-Library Plate.
-3. Sequencing Pool Tube.
-4. Sequencing Run Set.
+2. Extraction QC Plate.
+3. Sequencing-Library Plate.
+4. Sequencing Pool Tube.
+5. Sequencing Run Set.
+6. EUID Barcode Printing.
+7. Generic Set Management.
+8. Plate-Well Data.
+9. Spreadsheet Upload.
 
-It also has a generic EUID print panel and an action-results panel. Successful actions populate downstream fields where possible, for example extraction plate EUID into the library plate step and pool tube/content EUIDs into the run-set step.
+Successful actions populate downstream fields where possible, for example extraction plate EUID into the QC and library plate steps and pool tube/content EUIDs into the run-set step.
 
 ## Production Rollout Checklist
 
@@ -230,7 +339,7 @@ Use this checklist when updating production later.
    source ./activate 
    ruff check bloom_lims/api/v1/__init__.py bloom_lims/api/v1/lab_actions.py bloom_lims/api/v1/object_creation.py bloom_lims/api/v1/objects.py bloom_lims/domain/lab_actions.py bloom_lims/schemas/lab_actions.py bloom_lims/schemas/objects.py bloom_lims/gui/routes/modern.py tests/test_lab_actions_api.py tests/test_bloom_prefix_taxonomy.py
    python -m pytest tests/test_lab_actions_api.py tests/test_bloom_prefix_taxonomy.py::test_wet_lab_templates_use_bloom_prefix_taxonomy tests/test_route_coverage_gaps_api.py::test_object_creation_plate_creates_96_linked_wells tests/test_template_instantiation_recursion.py -q --no-cov
-   python -m pytest tests/test_lab_actions_api.py tests/test_bloom_prefix_taxonomy.py::test_wet_lab_templates_use_bloom_prefix_taxonomy tests/test_route_coverage_gaps_api.py::test_object_creation_plate_creates_96_linked_wells tests/test_template_instantiation_recursion.py tests/test_api_v1.py::TestObjectCreationAPI tests/test_api_v1.py::TestObjectCreationPathTraversal -q --cov-reset --cov=bloom_lims.api.v1.lab_actions --cov=bloom_lims.domain.lab_actions --cov=bloom_lims.schemas.lab_actions --cov=bloom_lims.api.v1.object_creation --cov=bloom_lims.schemas.objects --cov-report=term-missing --cov-report=json:coverage-lab-actions.json --cov-fail-under=81
+   python -m pytest tests/test_lab_actions_api.py tests/test_bloom_prefix_taxonomy.py::test_wet_lab_templates_use_bloom_prefix_taxonomy tests/test_route_coverage_gaps_api.py::test_object_creation_plate_creates_96_linked_wells tests/test_template_instantiation_recursion.py tests/test_api_v1.py::TestObjectCreationAPI tests/test_api_v1.py::TestObjectCreationPathTraversal -q --cov-reset --cov=bloom_lims.api.v1.lab_actions --cov=bloom_lims.domain.lab_actions --cov=bloom_lims.domain.lab_action_spreadsheets --cov=bloom_lims.schemas.lab_actions --cov=bloom_lims.api.v1.object_creation --cov=bloom_lims.schemas.objects --cov-report=term-missing --cov-report=json:coverage-lab-actions.json --cov-fail-under=81
    ```
 
 4. Release Bloom with an annotated semver tag.
diff --git a/docs/plans/20260618T190000Z_bloom_lab_action_spreadsheet_upload_ledger.md b/docs/plans/20260618T190000Z_bloom_lab_action_spreadsheet_upload_ledger.md
new file mode 100644
index 0000000..a3dd194
--- /dev/null
+++ b/docs/plans/20260618T190000Z_bloom_lab_action_spreadsheet_upload_ledger.md
@@ -0,0 +1,75 @@
+# Bloom Lab Actions Spreadsheet Upload Ledger
+
+Date: 2026-06-18
+
+## Summary
+
+Extend the existing Bloom lab-action layer so extraction QC plate fill, sequencing-library plate generation, plate-well associated data, pool creation from wells/tubes/contents/pools, generic set management, and sequencing run-set creation can be driven through API, GUI, and spreadsheet uploads.
+
+The attached workbook `Container to Container Interactions (1).xlsx` is a schema example. It has `Bulk Create`, `Transfer`, and `Annotation` sheets with source/target container, child container, content-template, and annotation/data-template columns. This pass supports that family of spreadsheet layout as a parsed/previewed container-interaction workbook and adds executable lab-action sheet shapes for the Bloom wet-lab flow.
+
+## Boundaries
+
+- Work stays in Bloom on `jem-dev`.
+- No production `day`, no `us-west-2`, no live deploy, no destructive DB repair.
+- Use existing TapDB generic instances and lineage records.
+- Do not revive queue or betalab workflow-driving behavior. Existing queue/betalab code may remain until replaced.
+- No fallback config discovery. Runtime config remains explicit.
+
+## Gate 0 Inventory
+
+| Surface | State |
+|---|---|
+| Branch | `jem-dev` |
+| Pre-existing dirty files | Untracked `coverage-lab-actions.json`, untracked `output/` |
+| Existing API | `/api/v1/lab-actions/extraction-plates`, `/seq-library-plates`, `/seq-library-pools`, `/seq-runs`, `/plates/{plate_euid}/mapping.csv`, `/print-euids` |
+| Existing GUI | `/lab-actions` wizard |
+| Existing templates | `set/run-set/generic/1.01`, recursive 96-well plate templates, gDNA, sequencing-library content, sequencing-library pool, sequencing-index, gDNA quant |
+| Spreadsheet example | Sheets: `Bulk Create`, `Transfer`, `Annotation`; headers on row 4 |
+
+## Workstreams
+
+| ID | Requirement | Status | Evidence |
+|---|---|---|---|
+| LEDGER-001 | Create ledger and record attached spreadsheet/current source baseline. | COMPLETE | This ledger records the workbook sheets, Bloom branch, pre-existing dirt, current lab-action API, GUI, and template baseline. |
+| XLSX-001 | Add dependency-free CSV/XLSX workbook parser for lab-action uploads. | COMPLETE | `bloom_lims/domain/lab_action_spreadsheets.py`; parser accepts `.csv` and `.xlsx`, normalizes operator header typos, and previews the attached workbook family. |
+| QC-001 | Add extraction QC plate fill API/domain support. | COMPLETE | `POST /api/v1/lab-actions/extraction-qc-plates`; `LabActionsService.fill_extraction_qc_plate`; tests cover explicit QC well fill and 96-assignment capacity guard. |
+| DATA-001 | Add associated data-to-plate-well API/domain support. | COMPLETE | `POST /api/v1/lab-actions/plate-well-data`; supports well or well-content targets with structured data payloads. |
+| SET-001 | Add generic set create/read/member-management API/domain support. | COMPLETE | `POST /sets`, `GET /sets/{set_euid}`, and `POST /sets/{set_euid}/members`; uses existing `set/run-set/generic/1.01` template and lineage. |
+| IMPORT-001 | Add spreadsheet upload endpoint that can dry-run/execute explicit lab-action sheets and preview container-interaction sheets. | COMPLETE | `POST /api/v1/lab-actions/spreadsheet-import`; tests execute extraction QC, seq-library plate, seq-pool, seq-run set, set, and plate-well-data CSV imports, and preview XLSX `Transfer`. |
+| GUI-001 | Expose QC, data, set, and spreadsheet-upload controls on `/lab-actions`. | COMPLETE | `templates/modern/lab_actions.html`; GUI smoke test confirms Extraction QC, Spreadsheet Upload, Manage Sets, and upload action controls render. |
+| DOC-001 | Update docs with sheet schemas, API routes, and production rollout guidance. | COMPLETE | `README.md`, `docs/apis.md`, `docs/gui.md`, and `docs/lab_actions.md` updated with endpoints, sheet schemas, GUI panels, and rollout tests. |
+| TEST-001 | Add focused parser/API/GUI tests and run validation. | COMPLETE | `ruff check ...` passed; `source ./activate dev && python -m pytest tests/test_lab_actions_api.py -q --no-cov` -> 13 passed; changed-surface coverage command -> 34 passed, total coverage 83.16% >= 81%. |
+| REPORT-001 | Final report with test output, changed files, and commit status. | COMPLETE | This ledger plus final chat report. Generated coverage/output artifacts are not committed unless promoted separately. |
+
+## Spreadsheet Sheet Shapes
+
+Executable lab-action uploads use these sheet names:
+
+- `Extraction Plate`
+- `Extraction QC`
+- `Seq Library Plate`
+- `Seq Pool`
+- `Seq Run Set`
+- `Sets`
+- `Plate Well Data`
+
+Container-interaction workbook sheets from the attached example are parsed for preview/evidence:
+
+- `Bulk Create`
+- `Transfer`
+- `Annotation`
+
+## Acceptance
+
+- API tests prove QC plate fill, plate-well data, set management, pool from plate well/tube, and spreadsheet import.
+- GUI smoke test proves the upload/QC/set controls render on `/lab-actions`.
+- Docs explain the spreadsheet columns and current production rollout boundary.
+- No queue-driving logic is added.
+
+## Validation
+
+- `python -m py_compile bloom_lims/domain/lab_action_spreadsheets.py bloom_lims/domain/lab_actions.py bloom_lims/api/v1/lab_actions.py bloom_lims/schemas/lab_actions.py` -> passed.
+- `ruff check bloom_lims/domain/lab_action_spreadsheets.py bloom_lims/domain/lab_actions.py bloom_lims/api/v1/lab_actions.py bloom_lims/schemas/lab_actions.py tests/test_lab_actions_api.py` -> passed.
+- `source ./activate dev && python -m pytest tests/test_lab_actions_api.py -q --no-cov` -> 13 passed.
+- `source ./activate dev && python -m pytest tests/test_lab_actions_api.py tests/test_bloom_prefix_taxonomy.py::test_wet_lab_templates_use_bloom_prefix_taxonomy tests/test_route_coverage_gaps_api.py::test_object_creation_plate_creates_96_linked_wells tests/test_template_instantiation_recursion.py tests/test_api_v1.py::TestObjectCreationAPI tests/test_api_v1.py::TestObjectCreationPathTraversal -q --cov-reset --cov=bloom_lims.api.v1.lab_actions --cov=bloom_lims.domain.lab_actions --cov=bloom_lims.domain.lab_action_spreadsheets --cov=bloom_lims.schemas.lab_actions --cov=bloom_lims.api.v1.object_creation --cov=bloom_lims.schemas.objects --cov-report=term-missing --cov-report=json:coverage-lab-actions.json --cov-fail-under=81` -> 34 passed, total coverage 83.16%.
diff --git a/templates/modern/lab_actions.html b/templates/modern/lab_actions.html
index c708dcb..6d6e731 100644
--- a/templates/modern/lab_actions.html
+++ b/templates/modern/lab_actions.html
@@ -78,7 +78,24 @@ 
1. Extraction Plate

 
     

         

-            
2. Sequencing-Library Plate

+            
2. Extraction QC Plate

+        

+        

+            
+            
+            
+            
+            
+            
+            
+        

+    

+
+    

+        

+            
3. Sequencing-Library Plate

         

         

             
@@ -93,7 +110,7 @@ 
2. Sequencing-Library Plate

 
     

         

-            
3. Sequencing Pool Tube

+            
4. Sequencing Pool Tube

         

         

             
@@ -118,7 +135,7 @@ 
3. Sequencing Pool Tube

 
     

         

-            
4. Sequencing Run Set

+            
5. Sequencing Run Set

         

         

             
@@ -136,6 +153,62 @@ 
4. Sequencing Run Set

     

 

 
+

+    

+        

+            
Manage Sets

+        

+        

+            
+            
+            
+            
+            
+            
+            
+        

+    

+
+    

+        

+            
Plate-Well Data

+        

+        

+            
+            
+            
+            
+            
+            
+            
+        

+    

+

+
+

+    

+        
Spreadsheet Upload

+    

+    

+        

+            Upload `.xlsx` or `.csv` sheets for Extraction Plate, Extraction QC, Seq Library Plate, Seq Pool,
+            Seq Run Set, Sets, or Plate Well Data. Bulk Create, Transfer, and Annotation sheets are parsed as previews.
+        

+        
+        
+        
+    

+

+
 

     

         
Print EUID Barcodes

@@ -203,12 +276,18 @@ 
Action Results

     if (payload.pool_tube_euid) {
       euids.push(payload.pool_tube_euid);
     }
+    if (payload.qc_plate_euid) {
+      euids.push(payload.qc_plate_euid);
+    }
     if (euids.length) {
       document.getElementById('print-euids').value = Array.from(new Set(euids)).join('\n');
     }
     if (payload.plate_euid && !document.getElementById('library-source-plate').value) {
       document.getElementById('library-source-plate').value = payload.plate_euid;
     }
+    if (payload.plate_euid && !document.getElementById('qc-source-plate').value) {
+      document.getElementById('qc-source-plate').value = payload.plate_euid;
+    }
     if (payload.mappings) {
       const libraryInputs = payload.mappings
         .map((item) => item.library_content_euid || item.output_content_euid)
@@ -246,6 +325,50 @@ 
Action Results

     return data;
   }
 
+  function assignmentRows(textareaId) {
+    return document.getElementById(textareaId).value
+      .split(/\r?\n/)
+      .map((line) => line.trim())
+      .filter(Boolean)
+      .map((line) => {
+        const [position, status, ...pairs] = line.split(',').map((value) => value.trim());
+        const match = position.match(/^([A-Ha-h])(\d{1,2})$/);
+        const data = {};
+        pairs.forEach((pair) => {
+          const [key, value] = pair.split('=');
+          if (key && value !== undefined) {
+            data[key.trim()] = value.trim();
+          }
+        });
+        return {
+          row: match ? match[1].toUpperCase() : null,
+          col: match ? Number(match[2]) : null,
+          status: status || null,
+          result: status || null,
+          data,
+        };
+      });
+  }
+
+  async function uploadSpreadsheet() {
+    const input = document.getElementById('spreadsheet-file');
+    if (!input.files.length) {
+      throw new Error('Choose a .xlsx or .csv file first');
+    }
+    const execute = document.getElementById('spreadsheet-execute').checked;
+    const form = new FormData();
+    form.append('file', input.files[0]);
+    const response = await fetch(`/api/v1/lab-actions/spreadsheet-import?dry_run=${execute ? 'false' : 'true'}`, {
+      method: 'POST',
+      body: form,
+    });
+    const data = await response.json().catch(() => ({detail: response.statusText}));
+    if (!response.ok) {
+      throw new Error(data.detail || response.statusText);
+    }
+    return data;
+  }
+
   const handlers = {
     'create-extraction': async () => postJson('/api/v1/lab-actions/extraction-plates', {
       mode: 'auto',
@@ -258,6 +381,11 @@ 
Action Results

       source_plate_euid: document.getElementById('library-source-plate').value.trim(),
       plate_name: document.getElementById('library-name').value || 'seq library plate',
     }),
+    'create-qc': async () => postJson('/api/v1/lab-actions/extraction-qc-plates', {
+      source_plate_euid: document.getElementById('qc-source-plate').value.trim(),
+      qc_plate_name: document.getElementById('qc-name').value || 'extraction QC plate',
+      assignments: assignmentRows('qc-assignments'),
+    }),
     'create-pool': async () => postJson('/api/v1/lab-actions/seq-library-pools', {
       input_euids: lines('pool-inputs'),
       platform: document.getElementById('pool-platform').value,
@@ -271,6 +399,23 @@ 
Action Results

       operator: document.getElementById('run-operator').value.trim(),
       status: 'created',
     }),
+    'create-set': async () => postJson('/api/v1/lab-actions/sets', {
+      name: document.getElementById('set-name').value.trim(),
+      members: lines('set-members'),
+      external_members: lines('set-external-members'),
+      status: 'created',
+    }),
+    'attach-data': async () => postJson('/api/v1/lab-actions/plate-well-data', {
+      data_template_code: document.getElementById('data-template').value.trim(),
+      records: assignmentRows('data-records').map((item) => ({
+        plate_euid: document.getElementById('data-plate').value.trim(),
+        row: item.row,
+        col: item.col,
+        target: 'content',
+        data: item.data,
+      })),
+    }),
+    'upload-spreadsheet': uploadSpreadsheet,
     'print-euids': async () => postJson('/api/v1/lab-actions/print-euids', {
       euids: lines('print-euids'),
       lab: document.getElementById('print-lab').value.trim(),
diff --git a/tests/test_lab_actions_api.py b/tests/test_lab_actions_api.py
index b5f3953..0e3f23f 100644
--- a/tests/test_lab_actions_api.py
+++ b/tests/test_lab_actions_api.py
@@ -3,6 +3,8 @@
 from __future__ import annotations
 
 import os
+import zipfile
+from io import BytesIO
 from unittest.mock import patch
 
 os.environ["BLOOM_DEV_AUTH_BYPASS"] = "true"
@@ -10,6 +12,7 @@
 
 from fastapi.testclient import TestClient
 
+from bloom_lims.domain.lab_action_spreadsheets import parse_workbook
 from main import app
 
 
@@ -564,3 +567,303 @@ def test_lab_action_schema_validation_edges() -> None:
         },
     )
     assert too_many_prints.status_code == 422
+
+
+def test_qc_plate_data_sets_and_pool_from_well_and_tube() -> None:
+    client = _client()
+    tube_1, _ = _create_filled_tube(client, suffix="qc-a")
+    tube_2, _ = _create_filled_tube(client, suffix="qc-b")
+
+    with patch(
+        "bloom_lims.integrations.atlas.events.emit_bloom_event", return_value=None
+    ):
+        extraction = client.post(
+            "/api/v1/lab-actions/extraction-plates",
+            json={
+                "mode": "auto",
+                "tube_euids": [tube_1],
+                "plate_name": "pytest spreadsheet extraction plate",
+            },
+        )
+    assert extraction.status_code == 200, extraction.text
+    extraction_payload = extraction.json()
+    source_well = extraction_payload["mappings"][0]["well_euid"]
+
+    qc = client.post(
+        "/api/v1/lab-actions/extraction-qc-plates",
+        json={
+            "source_plate_euid": extraction_payload["plate_euid"],
+            "qc_plate_name": "pytest extraction QC plate",
+            "assignments": [
+                {
+                    "source_well_euid": source_well,
+                    "qc_row": "A",
+                    "qc_col": 1,
+                    "result": "pass",
+                    "status": "recorded",
+                    "data": {"concentration_ng_ul": 12.3},
+                }
+            ],
+        },
+    )
+    assert qc.status_code == 200, qc.text
+    qc_payload = qc.json()
+    assert qc_payload["qc_plate_euid"]
+    assert qc_payload["mappings"][0]["result"] == "pass"
+    assert qc_payload["mappings"][0]["data_euid"]
+
+    data = client.post(
+        "/api/v1/lab-actions/plate-well-data",
+        json={
+            "data_template_code": "data/operation/extraction-qc/1.0/",
+            "records": [
+                {
+                    "plate_euid": extraction_payload["plate_euid"],
+                    "row": "A",
+                    "col": 1,
+                    "target": "content",
+                    "data": {"a260_280": 1.82},
+                }
+            ],
+        },
+    )
+    assert data.status_code == 200, data.text
+    assert data.json()["mappings"][0]["data_euid"]
+
+    lab_set = client.post(
+        "/api/v1/lab-actions/sets",
+        json={
+            "name": "pytest extraction set",
+            "members": [extraction_payload["plate_euid"], qc_payload["qc_plate_euid"]],
+            "external_members": ["external-reagent-lot-1"],
+        },
+    )
+    assert lab_set.status_code == 200, lab_set.text
+    set_euid = lab_set.json()["set_euid"]
+    add_members = client.post(
+        f"/api/v1/lab-actions/sets/{set_euid}/members",
+        json={"members": [tube_2], "external_members": ["operator-note-1"]},
+    )
+    assert add_members.status_code == 200, add_members.text
+    fetched = client.get(f"/api/v1/lab-actions/sets/{set_euid}")
+    assert fetched.status_code == 200
+    assert tube_2 in fetched.json()["members"]
+    assert "operator-note-1" in fetched.json()["external_members"]
+
+    with patch(
+        "bloom_lims.integrations.atlas.events.emit_bloom_event", return_value=None
+    ):
+        pool = client.post(
+            "/api/v1/lab-actions/seq-library-pools",
+            json={
+                "input_euids": [source_well, tube_2],
+                "platform": "ILMN",
+                "pool_name": "pytest well plus tube pool",
+            },
+        )
+    assert pool.status_code == 200, pool.text
+    assert len(pool.json()["member_euids"]) == 2
+
+
+def _minimal_xlsx(sheet_name: str, rows: list[list[str | None]]) -> bytes:
+    def cell_ref(row_index: int, col_index: int) -> str:
+        col = ""
+        value = col_index
+        while value:
+            value, remainder = divmod(value - 1, 26)
+            col = chr(65 + remainder) + col
+        return f"{col}{row_index}"
+
+    sheet_rows = []
+    for row_index, row in enumerate(rows, start=1):
+        cells = []
+        for col_index, value in enumerate(row, start=1):
+            if value is None:
+                continue
+            cells.append(
+                f'{value}'
+            )
+        sheet_rows.append(f'{"".join(cells)}')
+    worksheet = (
+        ''
+        ''
+        f'{"".join(sheet_rows)}'
+    )
+    output = BytesIO()
+    with zipfile.ZipFile(output, "w") as archive:
+        archive.writestr(
+            "[Content_Types].xml",
+            ''
+            ''
+            ''
+            ''
+            "",
+        )
+        archive.writestr(
+            "xl/workbook.xml",
+            ''
+            ''
+            f'',
+        )
+        archive.writestr(
+            "xl/_rels/workbook.xml.rels",
+            ''
+            ''
+            ''
+            "",
+        )
+        archive.writestr("xl/worksheets/sheet1.xml", worksheet)
+    return output.getvalue()
+
+
+def test_spreadsheet_import_csv_and_xlsx_preview() -> None:
+    client = _client()
+    tube, _ = _create_filled_tube(client, suffix="spreadsheet")
+    csv_bytes = (
+        "tube_euid,row,col,plate_name\n"
+        f"{tube},A,1,pytest upload extraction plate\n"
+    ).encode()
+    dry_run = client.post(
+        "/api/v1/lab-actions/spreadsheet-import",
+        params={"dry_run": "true"},
+        files={"file": ("extraction.csv", csv_bytes, "text/csv")},
+    )
+    assert dry_run.status_code == 200, dry_run.text
+    assert dry_run.json()["actions"][0]["action"] == "extraction_plate"
+    assert dry_run.json()["actions"][0]["request"]["mode"] == "directed"
+
+    with patch(
+        "bloom_lims.integrations.atlas.events.emit_bloom_event", return_value=None
+    ):
+        execute = client.post(
+            "/api/v1/lab-actions/spreadsheet-import",
+            params={"dry_run": "false"},
+            files={"file": ("extraction.csv", csv_bytes, "text/csv")},
+        )
+    assert execute.status_code == 200, execute.text
+    assert execute.json()["actions"][0]["result"]["plate_euid"]
+
+    workbook = _minimal_xlsx(
+        "Transfer",
+        [
+            [],
+            [],
+            ["SOURCE CONTAINER(s)", None, None, None, None, None, None, None, None, "DESTINATION CONTAINER(s)"],
+            ["Container EUID", "Container Template EUID", "Continer Cat/Type/Subtype"],
+            ["BCT-EXAMPLE", "container/tube/tube-generic-10ml/1.0", "container/tube/generic"],
+        ],
+    )
+    parsed = parse_workbook("container_interactions.xlsx", workbook)
+    assert parsed[0].name == "Transfer"
+    assert "container_euid" in parsed[0].headers
+    preview = client.post(
+        "/api/v1/lab-actions/spreadsheet-import",
+        params={"dry_run": "true"},
+        files={
+            "file": (
+                "container_interactions.xlsx",
+                workbook,
+                "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet",
+            )
+        },
+    )
+    assert preview.status_code == 200, preview.text
+    assert preview.json()["actions"][0]["action"] == "container_interaction_preview"
+
+
+def _upload_csv(client: TestClient, csv_text: str, *, dry_run: bool = False):
+    return client.post(
+        "/api/v1/lab-actions/spreadsheet-import",
+        params={"dry_run": str(dry_run).lower()},
+        files={"file": ("lab_action.csv", csv_text.encode(), "text/csv")},
+    )
+
+
+def test_spreadsheet_import_executes_each_lab_action_sheet_shape() -> None:
+    client = _client()
+    tube, _ = _create_filled_tube(client, suffix="upload-flow")
+    extraction = client.post(
+        "/api/v1/lab-actions/extraction-plates",
+        json={"mode": "auto", "tube_euids": [tube]},
+    )
+    assert extraction.status_code == 200, extraction.text
+    extraction_payload = extraction.json()
+    source_well = extraction_payload["mappings"][0]["well_euid"]
+
+    qc_csv = (
+        "source_well_euid,qc_row,qc_col,result,status,data_concentration_ng_ul\n"
+        f"{source_well},A,1,pass,recorded,11.2\n"
+    )
+    qc = _upload_csv(client, qc_csv)
+    assert qc.status_code == 200, qc.text
+    qc_action = qc.json()["actions"][0]
+    assert qc_action["action"] == "extraction_qc"
+    assert qc_action["result"]["mappings"][0]["result"] == "pass"
+
+    library_csv = (
+        "source_well_euid,row,col,index_barcode,data_cycles\n"
+        f"{source_well},A,1,ACGTACGT,8\n"
+    )
+    library = _upload_csv(client, library_csv)
+    assert library.status_code == 200, library.text
+    library_action = library.json()["actions"][0]
+    assert library_action["action"] == "seq_library_plate"
+    library_content = library_action["result"]["mappings"][0]["library_content_euid"]
+
+    pool_csv = (
+        "input_euids,platform,pool_name,pool_batch\n"
+        f"{library_content},ILMN,pytest upload pool,batch-1\n"
+    )
+    pool = _upload_csv(client, pool_csv)
+    assert pool.status_code == 200, pool.text
+    pool_action = pool.json()["actions"][0]
+    assert pool_action["action"] == "seq_pool"
+    pool_result = pool_action["result"]
+
+    run_csv = (
+        "pool_tube_euid,pool_content_euid,platform,operator,flowcell_barcode,status,run_batch\n"
+        f"{pool_result['pool_tube_euid']},{pool_result['pool_content_euid']},ILMN,pytest@example.com,FLOWCELL-UPLOAD,created,batch-1\n"
+    )
+    run = _upload_csv(client, run_csv)
+    assert run.status_code == 200, run.text
+    run_action = run.json()["actions"][0]
+    assert run_action["action"] == "seq_run_set"
+    assert run_action["result"]["set_euid"]
+
+    set_csv = (
+        "name,members,external_members,status,set_note\n"
+        f"pytest upload set,{extraction_payload['plate_euid']};{pool_result['pool_tube_euid']},lot:123,created,upload\n"
+    )
+    lab_set = _upload_csv(client, set_csv)
+    assert lab_set.status_code == 200, lab_set.text
+    set_action = lab_set.json()["actions"][0]
+    assert set_action["action"] == "sets"
+    assert set_action["result"][0]["set_euid"]
+
+    data_csv = (
+        "well_euid,data_template_code,target,name,annotation_value,metric_a260_280\n"
+        f"{source_well},data/operation/extraction-qc/1.0/,content,pytest uploaded data,ok,1.82\n"
+    )
+    data = _upload_csv(client, data_csv)
+    assert data.status_code == 200, data.text
+    data_action = data.json()["actions"][0]
+    assert data_action["action"] == "plate_well_data"
+    assert data_action["result"]["mappings"][0]["data_euid"]
+
+    bad_extension = client.post(
+        "/api/v1/lab-actions/spreadsheet-import",
+        files={"file": ("lab_action.txt", b"not,csv", "text/plain")},
+    )
+    assert bad_extension.status_code == 400
+    assert "must be .csv or .xlsx" in bad_extension.json()["detail"]
+
+
+def test_lab_actions_gui_renders_upload_qc_and_set_controls() -> None:
+    client = _client()
+    response = client.get("/lab-actions")
+    assert response.status_code == 200, response.text
+    assert "Extraction QC Plate" in response.text
+    assert "Spreadsheet Upload" in response.text
+    assert "Manage Sets" in response.text
+    assert 'data-action="upload-spreadsheet"' in response.text

From 0d57f0aef8ac6d91b18fc67fd44742f40d3073f2 Mon Sep 17 00:00:00 2001
From: John Major 
Date: Thu, 18 Jun 2026 10:55:37 -0700
Subject: [PATCH 39/47] Release 7.0.17

---
 bloom_lims/api/v1/lab_actions.py  |   6 +-
 bloom_lims/domain/lab_actions.py  |  63 ++++++++++++-
 templates/modern/lab_actions.html | 150 +++++++++++++++++++-----------
 tests/test_lab_actions_api.py     |  14 ++-
 4 files changed, 170 insertions(+), 63 deletions(-)

diff --git a/bloom_lims/api/v1/lab_actions.py b/bloom_lims/api/v1/lab_actions.py
index 591a32e..99191af 100644
--- a/bloom_lims/api/v1/lab_actions.py
+++ b/bloom_lims/api/v1/lab_actions.py
@@ -177,12 +177,12 @@ async def download_seq_run_sample_sheet(
 ):
     service = _service_for_user(user)
     try:
-        content = service.illumina_sample_sheet(set_euid)
+        content, filename, media_type = service.sequencing_sample_sheet_download(set_euid)
         return PlainTextResponse(
             content,
-            media_type="text/csv",
+            media_type=media_type,
             headers={
-                "Content-Disposition": f'attachment; filename="{set_euid}_SampleSheet.csv"'
+                "Content-Disposition": f'attachment; filename="{filename}"'
             },
         )
     except Exception as exc:
diff --git a/bloom_lims/domain/lab_actions.py b/bloom_lims/domain/lab_actions.py
index 6579bc1..9c55789 100644
--- a/bloom_lims/domain/lab_actions.py
+++ b/bloom_lims/domain/lab_actions.py
@@ -866,14 +866,10 @@ def plate_mapping_csv(self, plate_euid: str) -> str:
         writer.writerows(rows)
         return output.getvalue()
 
-    def illumina_sample_sheet(self, set_euid: str) -> str:
+    def sequencing_sample_sheet(self, set_euid: str) -> str:
         run_set = self._require(set_euid)
         props = self._props(run_set)
         platform = str(props.get("platform") or "").strip()
-        if platform != "ILMN":
-            raise ValueError(
-                f"Sample sheet download is only implemented for ILMN, not {platform or 'unknown'}"
-            )
         pool_content = self._require(str(props.get("pool_content_euid") or ""))
         library_inputs = [
             lineage.parent_instance
@@ -916,6 +912,26 @@ def illumina_sample_sheet(self, set_euid: str) -> str:
                     ),
                 }
             )
+        if platform == "ONT":
+            return self._ont_sample_sheet(run_set=run_set, props=props, data_rows=data_rows)
+        if platform != "ILMN":
+            raise ValueError(
+                f"Sample sheet download is implemented for ILMN and ONT, not {platform or 'unknown'}"
+            )
+        return self._illumina_sample_sheet(run_set=run_set, props=props, data_rows=data_rows)
+
+    def sequencing_sample_sheet_download(self, set_euid: str) -> tuple[str, str, str]:
+        run_set = self._require(set_euid)
+        props = self._props(run_set)
+        platform = str(props.get("platform") or "").strip()
+        content = self.sequencing_sample_sheet(set_euid)
+        if platform == "ONT":
+            return content, f"{set_euid}_ONT_manifest.tsv", "text/tab-separated-values"
+        return content, f"{set_euid}_{platform or 'sequencing'}_SampleSheet.csv", "text/csv"
+
+    def _illumina_sample_sheet(
+        self, *, run_set, props: dict[str, Any], data_rows: list[dict[str, str]]
+    ) -> str:
         output = io.StringIO()
         output.write("[Header]\n")
         output.write(f"RunSetEUID,{run_set.euid}\n")
@@ -929,6 +945,43 @@ def illumina_sample_sheet(self, set_euid: str) -> str:
         writer.writerows(data_rows)
         return output.getvalue()
 
+    def _ont_sample_sheet(
+        self, *, run_set, props: dict[str, Any], data_rows: list[dict[str, str]]
+    ) -> str:
+        output = io.StringIO()
+        fieldnames = [
+            "sample_id",
+            "alias",
+            "barcode",
+            "run_set_euid",
+            "library_euid",
+            "source_gdna_euid",
+            "source_specimen_content_euid",
+            "flowcell_barcode",
+            "operator",
+        ]
+        writer = csv.DictWriter(output, fieldnames=fieldnames, delimiter="\t")
+        writer.writeheader()
+        for row in data_rows:
+            description = json.loads(row.get("Description") or "{}")
+            writer.writerow(
+                {
+                    "sample_id": row.get("Sample_ID") or "",
+                    "alias": row.get("Sample_Name") or row.get("Sample_ID") or "",
+                    "barcode": row.get("index") or "",
+                    "run_set_euid": run_set.euid,
+                    "library_euid": description.get("library_euid") or row.get("Sample_ID") or "",
+                    "source_gdna_euid": description.get("source_gdna_euid") or "",
+                    "source_specimen_content_euid": description.get(
+                        "source_specimen_content_euid"
+                    )
+                    or "",
+                    "flowcell_barcode": props.get("flowcell_barcode") or "",
+                    "operator": props.get("operator") or "",
+                }
+            )
+        return output.getvalue()
+
     def _split_values(self, value: Any) -> list[str]:
         if value in (None, ""):
             return []
diff --git a/templates/modern/lab_actions.html b/templates/modern/lab_actions.html
index 6d6e731..71f4c2c 100644
--- a/templates/modern/lab_actions.html
+++ b/templates/modern/lab_actions.html
@@ -61,16 +61,16 @@ 
1. Extraction Plate

         

         

             
-            
+            
             

                 
-                
+            
             

             
-            
         

@@ -82,12 +82,12 @@ 
2. Extraction QC Plate

         

         

             
-            
+            
             
-            
+            
             
-            
-            
         

@@ -99,10 +99,12 @@ 
3. Sequencing-Library Plate

         

         

             
-            
+            
             
-            
-            
         

@@ -114,10 +116,10 @@ 
4. Sequencing Pool Tube

         

         

             
-            
+            
             

                 
-                
                     
                     
                     
@@ -126,8 +128,8 @@ 
4. Sequencing Pool Tube

                 
             

             
-            
-            
         

@@ -139,14 +141,22 @@ 
5. Sequencing Run Set

         

         

             
-            
+            
             
-            
+            
+            
+            
             
-            
+            
             
-            
-            
         

@@ -160,12 +170,12 @@ 
Manage Sets

         
         

             
-            
+            
             
-            
+            
             
-            
-            
         

@@ -177,12 +187,12 @@ 
Plate-Well Data

         
         

             
-            
+            
             
-            
+            
             
-            
-            
         

@@ -198,12 +208,12 @@ 
Spreadsheet Upload

             Upload `.xlsx` or `.csv` sheets for Extraction Plate, Extraction QC, Seq Library Plate, Seq Pool,
             Seq Run Set, Sets, or Plate Well Data. Bulk Create, Transfer, and Annotation sheets are parsed as previews.
         

-        
+        
         
-        
     
@@ -215,22 +225,22 @@ 
Print EUID Barcodes

     
     

         
-        
+        
         

             

                 
-                
+                
             

             

                 
-                
+                
             

             

                 
-                
+                
             

         

-        
     

@@ -242,7 +252,7 @@ 
Action Results

     
     

         
-        
{}

+        
{}

     

 
 {% endblock %}
@@ -265,7 +275,8 @@ 
Action Results

       links.appendChild(link(`/api/v1/lab-actions/plates/${payload.plate_euid}/mapping.csv`, 'Download plate CSV'));
     }
     if (payload.set_euid) {
-      links.appendChild(link(`/api/v1/lab-actions/seq-runs/${payload.set_euid}/samplesheet`, 'Download ILMN sample sheet'));
+      const platform = payload.platform || document.getElementById('run-platform').value || 'sequencing';
+      links.appendChild(link(`/api/v1/lab-actions/seq-runs/${payload.set_euid}/samplesheet`, `Download ${platform} sample sheet`));
     }
     const euids = [];
     ['new_container_euids', 'created_euids'].forEach((key) => {
@@ -325,6 +336,17 @@ 
Action Results

     return data;
   }
 
+  function keyValueData(pairs) {
+    const data = {};
+    pairs.forEach((pair) => {
+      const [key, value] = pair.split('=');
+      if (key && value !== undefined) {
+        data[key.trim()] = value.trim();
+      }
+    });
+    return data;
+  }
+
   function assignmentRows(textareaId) {
     return document.getElementById(textareaId).value
       .split(/\r?\n/)
@@ -333,19 +355,33 @@ 
Action Results

       .map((line) => {
         const [position, status, ...pairs] = line.split(',').map((value) => value.trim());
         const match = position.match(/^([A-Ha-h])(\d{1,2})$/);
-        const data = {};
-        pairs.forEach((pair) => {
-          const [key, value] = pair.split('=');
-          if (key && value !== undefined) {
-            data[key.trim()] = value.trim();
-          }
-        });
         return {
           row: match ? match[1].toUpperCase() : null,
           col: match ? Number(match[2]) : null,
           status: status || null,
           result: status || null,
-          data,
+          data: keyValueData(pairs),
+        };
+      });
+  }
+
+  function libraryAssignmentRows(textareaId) {
+    return document.getElementById(textareaId).value
+      .split(/\r?\n/)
+      .map((line) => line.trim())
+      .filter(Boolean)
+      .map((line) => {
+        const [sourceWellEuid, position, indexBarcode, indexEuid, ...pairs] = line
+          .split(',')
+          .map((value) => value.trim());
+        const match = (position || '').match(/^([A-Ha-h])(\d{1,2})$/);
+        return {
+          source_well_euid: sourceWellEuid,
+          row: match ? match[1].toUpperCase() : null,
+          col: match ? Number(match[2]) : null,
+          index_barcode: indexBarcode || null,
+          index_euid: indexEuid || null,
+          data: keyValueData(pairs),
         };
       });
   }
@@ -376,11 +412,21 @@ 
Action Results

       plate_name: document.getElementById('extract-name').value || 'extraction plate',
       create_run_set: document.getElementById('extract-run-set').checked,
     }),
-    'create-library': async () => postJson('/api/v1/lab-actions/seq-library-plates', {
-      mode: 'plate_1_to_1',
-      source_plate_euid: document.getElementById('library-source-plate').value.trim(),
-      plate_name: document.getElementById('library-name').value || 'seq library plate',
-    }),
+    'create-library': async () => {
+      const assignments = libraryAssignmentRows('library-assignments');
+      if (assignments.length) {
+        return postJson('/api/v1/lab-actions/seq-library-plates', {
+          mode: 'directed',
+          assignments,
+          plate_name: document.getElementById('library-name').value || 'seq library plate',
+        });
+      }
+      return postJson('/api/v1/lab-actions/seq-library-plates', {
+        mode: 'plate_1_to_1',
+        source_plate_euid: document.getElementById('library-source-plate').value.trim(),
+        plate_name: document.getElementById('library-name').value || 'seq library plate',
+      });
+    },
     'create-qc': async () => postJson('/api/v1/lab-actions/extraction-qc-plates', {
       source_plate_euid: document.getElementById('qc-source-plate').value.trim(),
       qc_plate_name: document.getElementById('qc-name').value || 'extraction QC plate',
@@ -394,7 +440,7 @@ 
Action Results

     'create-run': async () => postJson('/api/v1/lab-actions/seq-runs', {
       pool_tube_euid: document.getElementById('run-pool-tube').value.trim(),
       pool_content_euid: document.getElementById('run-pool-content').value.trim() || null,
-      platform: 'ILMN',
+      platform: document.getElementById('run-platform').value,
       flowcell_barcode: document.getElementById('run-flowcell').value.trim(),
       operator: document.getElementById('run-operator').value.trim(),
       status: 'created',
diff --git a/tests/test_lab_actions_api.py b/tests/test_lab_actions_api.py
index 0e3f23f..8a1b081 100644
--- a/tests/test_lab_actions_api.py
+++ b/tests/test_lab_actions_api.py
@@ -213,7 +213,7 @@ def test_lab_actions_full_ilmn_flow_and_csv_export() -> None:
         assert library_content in sample_sheet.text
 
 
-def test_lab_actions_validation_and_non_ilmn_samplesheet_rejection() -> None:
+def test_lab_actions_validation_and_ont_samplesheet_download() -> None:
     client = _client()
     invalid = client.post(
         "/api/v1/lab-actions/extraction-plates",
@@ -247,8 +247,12 @@ def test_lab_actions_validation_and_non_ilmn_samplesheet_rejection() -> None:
     sample_sheet = client.get(
         f"/api/v1/lab-actions/seq-runs/{run.json()['set_euid']}/samplesheet"
     )
-    assert sample_sheet.status_code == 400
-    assert "only implemented for ILMN" in sample_sheet.json()["detail"]
+    assert sample_sheet.status_code == 200, sample_sheet.text
+    assert sample_sheet.headers["content-type"].startswith("text/tab-separated-values")
+    assert "_ONT_manifest.tsv" in sample_sheet.headers["content-disposition"]
+    assert "sample_id\talias\tbarcode\trun_set_euid" in sample_sheet.text
+    assert run.json()["set_euid"] in sample_sheet.text
+    assert "ONT-FLOWCELL" in sample_sheet.text
 
 
 def test_object_creation_count_and_print_euid_mock() -> None:
@@ -310,6 +314,10 @@ def test_lab_actions_gui_renders_wizard() -> None:
     assert "Sequencing Pool Tube" in html
     assert "Sequencing Run Set" in html
     assert "/api/v1/lab-actions/extraction-plates" in html
+    assert 'data-testid="bloom-lab-library-assignments"' in html
+    assert 'data-testid="bloom-lab-run-platform"' in html
+    assert "mode: 'directed'" in html
+    assert "Download ${platform} sample sheet" in html
 
 
 def test_directed_extraction_into_existing_plate_with_quant_and_reuse_guard() -> None:

From 5861cb33d2b2159d66c4e000bb72b10fe2aa46f5 Mon Sep 17 00:00:00 2001
From: John Major 
Date: Thu, 18 Jun 2026 15:54:26 -0700
Subject: [PATCH 40/47] Complete Bloom lab-action live proof support

---
 bloom_lims/domain/lab_actions.py  | 81 ++++++++++++++++++++++++++++++-
 bloom_lims/schemas/lab_actions.py |  1 +
 templates/modern/lab_actions.html |  5 ++
 tests/test_lab_actions_api.py     | 10 +++-
 4 files changed, 93 insertions(+), 4 deletions(-)

diff --git a/bloom_lims/domain/lab_actions.py b/bloom_lims/domain/lab_actions.py
index 9c55789..1b1fc6c 100644
--- a/bloom_lims/domain/lab_actions.py
+++ b/bloom_lims/domain/lab_actions.py
@@ -46,6 +46,9 @@
 POOL_CONTENT_TEMPLATE_CODE = "content/pool/sequencing-library/1.0/"
 GDNA_QUANT_TEMPLATE_CODE = "data/quantification/gdna/1.0/"
 EXTRACTION_QC_TEMPLATE_CODE = "data/operation/extraction-qc/1.0/"
+SEQUENCED_LIBRARY_ASSIGNMENT_TEMPLATE_CODE = (
+    "data/library-index-assignment/sequencing-library/1.0/"
+)
 
 
 def re_split_multi(value: str) -> list[str]:
@@ -795,6 +798,11 @@ def create_seq_run_set(self, request: SeqRunSetRequest) -> dict[str, Any]:
             self._create_lineage(run_set.euid, request.instrument_euid, "run_uses_instrument")
         for reagent_euid in request.reagent_euids:
             self._create_lineage(run_set.euid, reagent_euid, "run_uses_reagent")
+        assignments = self._create_sequenced_library_assignments(
+            run_set=run_set,
+            pool_content=pool_content,
+            flowcell_barcode=request.flowcell_barcode,
+        )
         self.bdb.session.commit()
         return {
             "set_euid": run_set.euid,
@@ -802,8 +810,65 @@ def create_seq_run_set(self, request: SeqRunSetRequest) -> dict[str, Any]:
             "platform": request.platform,
             "pool_tube_euid": pool_tube.euid,
             "pool_content_euid": pool_content.euid,
+            "assignments": assignments,
         }
 
+    def _create_sequenced_library_assignments(
+        self,
+        *,
+        run_set,
+        pool_content,
+        flowcell_barcode: str,
+    ) -> list[dict[str, str]]:
+        assignments: list[dict[str, str]] = []
+        source_libraries = [
+            lineage.parent_instance
+            for lineage in self._lineages_to_child(pool_content, "DERIVED_FROM")
+        ]
+        for index, library in enumerate(source_libraries, start=1):
+            props = self._props(library)
+            barcode = str(props.get("index_barcode") or "").strip()
+            lane = str(props.get("lane") or props.get("lane_index") or "1").strip()
+            assignment = self._create_by_code(
+                SEQUENCED_LIBRARY_ASSIGNMENT_TEMPLATE_CODE,
+                name=f"{run_set.euid}:{lane}:{barcode or library.euid}",
+                properties={
+                    "flowcell_id": flowcell_barcode,
+                    "lane": lane,
+                    "library_barcode": barcode,
+                    "library_prep_output_euid": library.euid,
+                    "library_material_euid": library.euid,
+                    "barcode_reagent_euid": str(props.get("index_euid") or "").strip(),
+                    "metadata": {
+                        "created_by": "bloom_lab_actions",
+                        "pool_content_euid": pool_content.euid,
+                    },
+                },
+            )
+            self._create_lineage(
+                run_set.euid,
+                assignment.euid,
+                "beta_sequenced_library_assignment",
+            )
+            self._create_lineage(
+                library.euid,
+                assignment.euid,
+                "beta_assignment_source",
+                edge_type="RUN_CONSUMED",
+                source_role="sequencing_run_set",
+                target_role="library_material",
+            )
+            assignments.append(
+                {
+                    "assignment_euid": assignment.euid,
+                    "library_content_euid": library.euid,
+                    "flowcell_id": flowcell_barcode,
+                    "lane": lane,
+                    "library_barcode": barcode,
+                }
+            )
+        return assignments
+
     def plate_mapping_rows(self, plate_euid: str) -> list[dict[str, str]]:
         plate = self._require(plate_euid)
         wells = self._plate_wells(plate)
@@ -1302,10 +1367,22 @@ def import_spreadsheet(
         return {"filename": filename, "dry_run": dry_run, "actions": actions}
 
     def print_euids(self, request: PrintEuidRequest) -> dict[str, Any]:
-        service = ZebraDayService()
         results = []
         for euid in request.euids:
             self._require(euid)
+            if request.dry_run:
+                results.append(
+                    {
+                        "dry_run": True,
+                        "lab": request.lab,
+                        "printer_id": request.printer_id,
+                        "label_zpl_style": request.label_zpl_style,
+                        "euid": euid,
+                        "copies": request.copies,
+                    }
+                )
+                continue
+            service = ZebraDayService()
             results.append(
                 service.submit_print_job(
                     lab=request.lab,
@@ -1315,4 +1392,4 @@ def print_euids(self, request: PrintEuidRequest) -> dict[str, Any]:
                     print_n=request.copies,
                 )
             )
-        return {"printed": len(results), "results": results}
+        return {"printed": 0 if request.dry_run else len(results), "dry_run": request.dry_run, "results": results}
diff --git a/bloom_lims/schemas/lab_actions.py b/bloom_lims/schemas/lab_actions.py
index 73c281c..9757601 100644
--- a/bloom_lims/schemas/lab_actions.py
+++ b/bloom_lims/schemas/lab_actions.py
@@ -260,6 +260,7 @@ class PrintEuidRequest(BaseModel):
     printer_id: str
     label_zpl_style: str
     copies: int = Field(default=1, ge=1, le=20)
+    dry_run: bool = False
 
     @field_validator("euids")
     @classmethod
diff --git a/templates/modern/lab_actions.html b/templates/modern/lab_actions.html
index 71f4c2c..729f562 100644
--- a/templates/modern/lab_actions.html
+++ b/templates/modern/lab_actions.html
@@ -240,6 +240,10 @@ 
Print EUID Barcodes

                 
             
         
+        
         
@@ -468,6 +472,7 @@ 
Action Results

       printer_id: document.getElementById('print-printer').value.trim(),
       label_zpl_style: document.getElementById('print-style').value.trim(),
       copies: 1,
+      dry_run: document.getElementById('print-dry-run').checked,
     }),
   };
 
diff --git a/tests/test_lab_actions_api.py b/tests/test_lab_actions_api.py
index 8a1b081..764a4d0 100644
--- a/tests/test_lab_actions_api.py
+++ b/tests/test_lab_actions_api.py
@@ -201,6 +201,9 @@ def test_lab_actions_full_ilmn_flow_and_csv_export() -> None:
     assert seq_run.status_code == 200, seq_run.text
     run_payload = seq_run.json()
     assert run_payload["set_euid"]
+    assert run_payload["assignments"]
+    assert run_payload["assignments"][0]["flowcell_id"] == "PYTEST-FLOWCELL"
+    assert run_payload["assignments"][0]["lane"] == "1"
 
     sample_sheet = client.get(
         f"/api/v1/lab-actions/seq-runs/{run_payload['set_euid']}/samplesheet"
@@ -282,11 +285,14 @@ def test_object_creation_count_and_print_euid_mock() -> None:
                 "printer_id": "pytest-printer",
                 "label_zpl_style": "euid",
                 "copies": 1,
+                "dry_run": True,
             },
         )
     assert response.status_code == 200, response.text
-    assert response.json()["printed"] == 3
-    assert service.submit_print_job.call_count == 3
+    assert response.json()["printed"] == 0
+    assert response.json()["dry_run"] is True
+    assert service.submit_print_job.call_count == 0
+    assert len(response.json()["results"]) == 3
 
     recursive_batch = client.post(
         "/api/v1/object-creation/create",

From 56d2961da56859b3b77e521f1e68c107e5c32472 Mon Sep 17 00:00:00 2001
From: John Major 
Date: Thu, 18 Jun 2026 16:51:54 -0700
Subject: [PATCH 41/47] Return plate identifiers from lab-action data attach

---
 bloom_lims/domain/lab_actions.py | 7 +++++++
 tests/test_lab_actions_api.py    | 6 +++++-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/bloom_lims/domain/lab_actions.py b/bloom_lims/domain/lab_actions.py
index 1b1fc6c..99fcbdc 100644
--- a/bloom_lims/domain/lab_actions.py
+++ b/bloom_lims/domain/lab_actions.py
@@ -476,8 +476,11 @@ def fill_extraction_qc_plate(
 
     def attach_plate_well_data(self, request: PlateWellDataRequest) -> dict[str, Any]:
         mappings: list[dict[str, Any]] = []
+        plate_euids: set[str] = set()
         for record in request.records:
             well = self._well_for_data_record(record)
+            if record.plate_euid:
+                plate_euids.add(record.plate_euid)
             target = well if record.target == "well" else self._well_content(well)
             data = self._create_by_code(
                 request.data_template_code,
@@ -493,6 +496,7 @@ def attach_plate_well_data(self, request: PlateWellDataRequest) -> dict[str, Any
             mappings.append(
                 {
                     "well_euid": well.euid,
+                    "plate_euid": record.plate_euid,
                     "target_euid": target.euid,
                     "data_euid": data.euid,
                     "relationship_type": request.relationship_type,
@@ -505,7 +509,10 @@ def attach_plate_well_data(self, request: PlateWellDataRequest) -> dict[str, Any
             member_euids=[item["data_euid"] for item in mappings],
         )
         self.bdb.session.commit()
+        sorted_plate_euids = sorted(plate_euids)
         return {
+            "plate_euid": sorted_plate_euids[0] if len(sorted_plate_euids) == 1 else None,
+            "plate_euids": sorted_plate_euids,
             "run_set_euid": run_set.euid if run_set is not None else None,
             "mappings": mappings,
         }
diff --git a/tests/test_lab_actions_api.py b/tests/test_lab_actions_api.py
index 764a4d0..011a05b 100644
--- a/tests/test_lab_actions_api.py
+++ b/tests/test_lab_actions_api.py
@@ -642,7 +642,11 @@ def test_qc_plate_data_sets_and_pool_from_well_and_tube() -> None:
         },
     )
     assert data.status_code == 200, data.text
-    assert data.json()["mappings"][0]["data_euid"]
+    data_payload = data.json()
+    assert data_payload["plate_euid"] == extraction_payload["plate_euid"]
+    assert data_payload["plate_euids"] == [extraction_payload["plate_euid"]]
+    assert data_payload["mappings"][0]["plate_euid"] == extraction_payload["plate_euid"]
+    assert data_payload["mappings"][0]["data_euid"]
 
     lab_set = client.post(
         "/api/v1/lab-actions/sets",

From 2d330b9726a51cbd64152590031c889aaf78fb5d Mon Sep 17 00:00:00 2001
From: John Major 
Date: Thu, 18 Jun 2026 17:32:40 -0700
Subject: [PATCH 42/47] Record live lab action E2E proof

---
 ...18T000000Z_bloom_lab_action_flow_ledger.md | 33 +++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/docs/plans/20260618T000000Z_bloom_lab_action_flow_ledger.md b/docs/plans/20260618T000000Z_bloom_lab_action_flow_ledger.md
index 8144825..a2befa9 100644
--- a/docs/plans/20260618T000000Z_bloom_lab_action_flow_ledger.md
+++ b/docs/plans/20260618T000000Z_bloom_lab_action_flow_ledger.md
@@ -81,3 +81,36 @@ Build a Bloom-owned lab actions layer for extraction plates, sequencing library
 - No real Zebra Day print job was sent.
 - Bloom release, Dayhoff pin update, and Dayhoff double-release are tracked in `dayhoff/docs/plans/20260618T131619Z_bloom_lab_actions_release_train_ledger.md`.
 - No live `jemdev5` refresh was performed in this pass.
+
+## 2026-06-19 Live `jemdev5` Proof
+
+The lab-action flow was released as Bloom `7.0.19`, pinned by Dayhoff `7.0.74`,
+self-pinned by Dayhoff `7.0.75`, and exercised in the live `jemdev5`
+greenfield hybrid GUI E2E run.
+
+| Surface | Live evidence |
+|---|---|
+| Deploy verification | `/Users/jmajor/projects/mega_dayhoff/dayhoff/output/jemdev5_verify_7_0_75_final/deploy-verify.md` |
+| GUI E2E screenshot pack | `/Users/jmajor/projects/mega_dayhoff/dayhoff/output/playwright/hybrid_order_to_delivery/hybrid_order_to_delivery/codex-hybrid-e2e-20260619T002814Z/` |
+| Tracked evidence guide | `/Users/jmajor/projects/mega_dayhoff/dayhoff/docs/evidence/hybrid_order_to_delivery_gui_e2e.md` |
+| Pytest result | `1 passed in 149.11s` |
+
+Live Bloom lab-action EUIDs from the passing run:
+
+| Role | EUID |
+|---|---|
+| Patient biospecimen tube | `Z-BCT-2AM` |
+| Extraction plate | `Z-BCP-19Z` |
+| Extraction well | `Z-BCW-3EN3` |
+| Extraction gDNA content | `Z-BNG-FX` |
+| ILMN prep set | `Z-BGS-15X` |
+| ONT prep set | `Z-BGS-16V` |
+| ILMN library plate | `Z-BCP-1AX` |
+| ONT library plate | `Z-BCP-1BV` |
+| ILMN pool tube | `Z-BCT-2BJ` |
+| ONT pool tube | `Z-BCT-2CG` |
+| ILMN seq-run set | `Z-BGS-17S` |
+| ONT seq-run set | `Z-BGS-18Q` |
+
+All Bloom lab-action rows are source-tested, release-pinned, deployed to
+`jemdev5`, and live-proven. Final status: `100%`.

From 94f0898f750d3d068eeb6d809bfe921fff23878c Mon Sep 17 00:00:00 2001
From: John Major 
Date: Fri, 19 Jun 2026 04:08:45 -0700
Subject: [PATCH 43/47] Fix TapDB semantic template categories

---
 README.md                                     |    4 +-
 bloom_lims/anomalies.py                       |    2 +-
 bloom_lims/auth/repositories/tapdb/groups.py  |    4 +-
 .../repositories/tapdb/user_api_tokens.py     |    4 +-
 bloom_lims/cli/db.py                          |   20 +-
 bloom_lims/config/container/tube.json         |    8 +-
 bloom_lims/config/container/well.json         |    2 +-
 bloom_lims/config/workflow_step/analysis.json |   16 +-
 .../workflow_step/extraction-steps.json       |   56 +-
 bloom_lims/domain/beta_lab.py                 |    8 +-
 bloom_lims/domain/execution_queue.py          |   32 +-
 bloom_lims/domain/lab_actions.py              |    6 +-
 bloom_lims/schemas/beta_lab.py                |    2 +-
 bloom_lims/schemas/external_specimens.py      |    2 +-
 config/tapdb_templates/bloom/templates.json   | 1342 ++++++++---------
 docs/apis.md                                  |    2 +-
 docs/lab_actions.md                           |   12 +-
 docs/old_docs/ATLAS_BLOOM_CONTRACT_TESTS.md   |    2 +-
 docs/old_docs/TAPDB_SPECIFICATION.md          |    2 +-
 ...520T064952Z_bloom_sequencing_run_ledger.md |    4 +-
 ...18T000000Z_bloom_lab_action_flow_ledger.md |   28 +-
 pyproject.toml                                |    2 +-
 tests/test_atlas_workflow_contract.py         |    8 +-
 tests/test_bloom_prefix_taxonomy.py           |   33 +-
 tests/test_cli_db_command_paths.py            |   33 +-
 tests/test_core_validation.py                 |    2 +-
 tests/test_packaging_metadata.py              |    2 +-
 tests/test_sequencing_run_contract.py         |    2 +-
 uv.lock                                       |    6 +-
 29 files changed, 833 insertions(+), 813 deletions(-)

diff --git a/README.md b/README.md
index b337713..24a494e 100644
--- a/README.md
+++ b/README.md
@@ -21,10 +21,12 @@
 
 Bloom is the LSMC internal material and container graph service. It owns laboratory containers, materials/content, equipment, lineage, recursive template creation, search, and graph views. Atlas owns orders and customer-facing accession context; Bloom owns the physical/material execution graph.
 
-Current Dayhoff pin: `7.0.16`. Current TapDB dependency: `daylily-tapdb @ ...@9.0.5`.
+Current Dayhoff pin: `7.0.20`. Current TapDB dependency: `daylily-tapdb @ ...@9.0.6`.
 
 Bloom is internal-only in Dayhoff exposure policy. It must be reachable only through approved LSMC networks and Dayhoff-generated service credentials.
 
+TapDB template identity is semantic. Categories are names like `container`, `material`, `data`, `equipment`, `set`, and `workflow`; prefixes such as `BC*`, `BN*`, `BD*`, `BR*`, and `BG*` are issuance and governance labels only. Existing historical objects keep their already minted EUIDs, but new and active template definitions must not use a Meridian/EUID prefix as the category name.
+
 ## What It Does
 
 - Owns Bloom containers, materials/content, equipment, recursive templates, lineages, search, and graph views.
diff --git a/bloom_lims/anomalies.py b/bloom_lims/anomalies.py
index 9ee96d0..9684423 100644
--- a/bloom_lims/anomalies.py
+++ b/bloom_lims/anomalies.py
@@ -15,7 +15,7 @@
 from bloom_lims.config import get_settings
 from bloom_lims.observability import ProjectionMetadata
 
-ANOMALY_TEMPLATE_CODE = "BAN/ops/anomaly-record/1.0/"
+ANOMALY_TEMPLATE_CODE = "ops/anomaly-record/generic/1.0/"
 ANOMALY_PREFIX = "BAN"
 
 
diff --git a/bloom_lims/auth/repositories/tapdb/groups.py b/bloom_lims/auth/repositories/tapdb/groups.py
index 19a87dd..2c30f5b 100644
--- a/bloom_lims/auth/repositories/tapdb/groups.py
+++ b/bloom_lims/auth/repositories/tapdb/groups.py
@@ -22,8 +22,8 @@
 )
 from bloom_lims.config import get_settings
 
-GROUP_TEMPLATE_CODE = "BBX/auth/user-group/1.0/"
-GROUP_MEMBERSHIP_TEMPLATE_CODE = "BBX/auth/user-group-membership/1.0/"
+GROUP_TEMPLATE_CODE = "auth/user-group/generic/1.0/"
+GROUP_MEMBERSHIP_TEMPLATE_CODE = "auth/user-group-membership/generic/1.0/"
 
 GROUP_PREFIX = "BBX"
 GROUP_MEMBERSHIP_PREFIX = "BBX"
diff --git a/bloom_lims/auth/repositories/tapdb/user_api_tokens.py b/bloom_lims/auth/repositories/tapdb/user_api_tokens.py
index d59d853..49df31f 100644
--- a/bloom_lims/auth/repositories/tapdb/user_api_tokens.py
+++ b/bloom_lims/auth/repositories/tapdb/user_api_tokens.py
@@ -22,8 +22,8 @@
 )
 from bloom_lims.config import get_settings
 
-TOKEN_TEMPLATE_CODE = "BBX/auth/user-api-token/1.0/"
-TOKEN_USAGE_LOG_TEMPLATE_CODE = "BBX/auth/user-api-token-usage-log/1.0/"
+TOKEN_TEMPLATE_CODE = "auth/user-api-token/generic/1.0/"
+TOKEN_USAGE_LOG_TEMPLATE_CODE = "auth/user-api-token-usage-log/generic/1.0/"
 
 TOKEN_PREFIX = "BBX"
 TOKEN_USAGE_PREFIX = "BBX"
diff --git a/bloom_lims/cli/db.py b/bloom_lims/cli/db.py
index 5d3107d..dd8859a 100644
--- a/bloom_lims/cli/db.py
+++ b/bloom_lims/cli/db.py
@@ -383,7 +383,12 @@ def _retire_obsolete_template_variants(
     domain_code: str,
 ) -> int:
     current = _active_template_categories_by_semantic_key(templates)
-    if not current:
+    current_prefixes = {
+        str(template.get("instance_prefix") or "").strip().upper()
+        for template in templates
+        if str(template.get("instance_prefix") or "").strip()
+    }
+    if not current and not current_prefixes:
         return 0
 
     rows = (
@@ -405,9 +410,20 @@ def _retire_obsolete_template_variants(
                 str(row.version or "").strip(),
             )
             expected_category = current.get(key)
+            actual_category = str(row.category or "").strip().upper()
+            semantic_category = template_semantic_category(row).strip().upper()
+            if semantic_category and actual_category != semantic_category:
+                row.is_deleted = True
+                row.bstatus = "retired"
+                retired += 1
+                continue
+            if actual_category in current_prefixes:
+                row.is_deleted = True
+                row.bstatus = "retired"
+                retired += 1
+                continue
             if expected_category is None:
                 continue
-            actual_category = str(row.category or "").strip().upper()
             if actual_category == expected_category:
                 continue
             row.is_deleted = True
diff --git a/bloom_lims/config/container/tube.json b/bloom_lims/config/container/tube.json
index 7b7fdc4..d38a26b 100644
--- a/bloom_lims/config/container/tube.json
+++ b/bloom_lims/config/container/tube.json
@@ -39,7 +39,7 @@
         "name": "10ml glass tube"
       },
       "valid_content": [
-        "content/.*"
+        "material/.*"
       ],
       "valid_parents": []
     }
@@ -84,7 +84,7 @@
         "name": "1.5ml eppi tube"
       },
       "valid_content": [
-        "content/.*"
+        "material/.*"
       ],
       "valid_parents": []
     }
@@ -129,7 +129,7 @@
         "name": "10ml tube generic"
       },
       "valid_content": [
-        "content/.*"
+        "material/.*"
       ],
       "valid_parents": []
     }
@@ -175,7 +175,7 @@
       },
       "singleton": "0",
       "valid_content": [
-        "content/.*"
+        "material/.*"
       ],
       "valid_parents": []
     }
diff --git a/bloom_lims/config/container/well.json b/bloom_lims/config/container/well.json
index a9d6e1b..77e7f58 100644
--- a/bloom_lims/config/container/well.json
+++ b/bloom_lims/config/container/well.json
@@ -36,7 +36,7 @@
       },
       "singleton": "0",
       "valid_content": [
-        "content/.*"
+        "material/.*"
       ],
       "valid_parents": [
         "container/plate/fixed-plate.*?/.*?"
diff --git a/bloom_lims/config/workflow_step/analysis.json b/bloom_lims/config/workflow_step/analysis.json
index d815f0c..44973f7 100644
--- a/bloom_lims/config/workflow_step/analysis.json
+++ b/bloom_lims/config/workflow_step/analysis.json
@@ -22,44 +22,44 @@
       "expected_inputs": [
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         }
       ],
       "expected_outputs": [
         {
           "container/tube/tube-generic-10ml/*/": {
-            "holds_content": "content/sample/blood-plasma/*"
+            "holds_content": "material/sample/blood-plasma/*"
           }
         },
         {
           "container/tube/tube-generic-10ml/*/": {
-            "holds_content": "content/sample/blood-plasma/*"
+            "holds_content": "material/sample/blood-plasma/*"
           }
         },
         {
           "container/tube/tube-generic-10ml/*/": {
-            "holds_content": "content/sample/blood-plasma/*"
+            "holds_content": "material/sample/blood-plasma/*"
           }
         },
         {
           "container/tube/tube-generic-10ml/*/": {
-            "holds_content": "content/sample/blood-plasma/*"
+            "holds_content": "material/sample/blood-plasma/*"
           }
         }
       ],
diff --git a/bloom_lims/config/workflow_step/extraction-steps.json b/bloom_lims/config/workflow_step/extraction-steps.json
index 925c5e6..ff54b1d 100644
--- a/bloom_lims/config/workflow_step/extraction-steps.json
+++ b/bloom_lims/config/workflow_step/extraction-steps.json
@@ -24,22 +24,22 @@
         [
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           },
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           },
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           },
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           }
         ]
@@ -51,7 +51,7 @@
               "child_of_lineages": [
                 {
                   "container/well/fixed-plate-well/*/": {
-                    "holds_content": "content/sample/cfdna/*"
+                    "holds_content": "material/sample/cfdna/*"
                   }
                 }
               ]
@@ -62,7 +62,7 @@
               "child_of_lineages": [
                 {
                   "container/well/fixed-plate-well/*/": {
-                    "holds_content": "content/sample/cfdna/*"
+                    "holds_content": "material/sample/cfdna/*"
                   }
                 }
               ]
@@ -73,7 +73,7 @@
               "child_of_lineages": [
                 {
                   "container/well/fixed-plate-well/*/": {
-                    "holds_content": "content/sample/cfdna/*"
+                    "holds_content": "material/sample/cfdna/*"
                   }
                 }
               ]
@@ -84,7 +84,7 @@
               "child_of_lineages": [
                 {
                   "container/well/fixed-plate-well/*/": {
-                    "holds_content": "content/sample/cfdna/*"
+                    "holds_content": "material/sample/cfdna/*"
                   }
                 }
               ]
@@ -133,22 +133,22 @@
       "expected_inputs": [
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         }
       ],
@@ -159,7 +159,7 @@
               "child_of_lineages": [
                 {
                   "container/well/fixed-plate-well/*/": {
-                    "holds_content": "content/sample/gdna/*"
+                    "holds_content": "material/sample/gdna/*"
                   }
                 }
               ]
@@ -170,7 +170,7 @@
               "child_of_lineages": [
                 {
                   "container/well/fixed-plate-well/*/": {
-                    "holds_content": "content/sample/gdna/*"
+                    "holds_content": "material/sample/gdna/*"
                   }
                 }
               ]
@@ -181,7 +181,7 @@
               "child_of_lineages": [
                 {
                   "container/well/fixed-plate-well/*/": {
-                    "holds_content": "content/sample/gdna/*"
+                    "holds_content": "material/sample/gdna/*"
                   }
                 }
               ]
@@ -192,7 +192,7 @@
               "child_of_lineages": [
                 {
                   "container/well/fixed-plate-well/*/": {
-                    "holds_content": "content/sample/gdna/*"
+                    "holds_content": "material/sample/gdna/*"
                   }
                 }
               ]
@@ -241,22 +241,22 @@
       "expected_inputs": [
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         }
       ],
@@ -302,44 +302,44 @@
       "expected_inputs": [
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         },
         {
           "container/tube/tube-strek-10ml/*/": {
-            "holds_content": "content/specimen/blood-whole/*"
+            "holds_content": "material/specimen/blood-whole/*"
           }
         }
       ],
       "expected_outputs": [
         {
           "container/tube/tube-generic-10ml/*/": {
-            "holds_content": "content/sample/blood-plasma/*"
+            "holds_content": "material/sample/blood-plasma/*"
           }
         },
         {
           "container/tube/tube-generic-10ml/*/": {
-            "holds_content": "content/sample/blood-plasma/*"
+            "holds_content": "material/sample/blood-plasma/*"
           }
         },
         {
           "container/tube/tube-generic-10ml/*/": {
-            "holds_content": "content/sample/blood-plasma/*"
+            "holds_content": "material/sample/blood-plasma/*"
           }
         },
         {
           "container/tube/tube-generic-10ml/*/": {
-            "holds_content": "content/sample/blood-plasma/*"
+            "holds_content": "material/sample/blood-plasma/*"
           }
         }
       ],
diff --git a/bloom_lims/domain/beta_lab.py b/bloom_lims/domain/beta_lab.py
index 1c1a4b4..3a377ce 100644
--- a/bloom_lims/domain/beta_lab.py
+++ b/bloom_lims/domain/beta_lab.py
@@ -60,10 +60,10 @@ class BetaLabService(
     REL_MATERIAL_CONSUMPTION = "beta_material_consumption"
     REL_USED_INSTRUMENT = "beta_used_instrument"
     REL_USED_REAGENT = "beta_used_reagent"
-    POOL_TEMPLATE_CODE = "content/pool/sequencing-library/1.0"
+    POOL_TEMPLATE_CODE = "material/pool/sequencing-library/1.0"
     POOL_CONTAINER_TEMPLATE_CODE = "container/tube/tube-generic-10ml/1.0"
     LIBRARY_PREP_OUTPUT_TEMPLATE_CODE = "data/operation/library-prep/1.0"
-    LIBRARY_MATERIAL_TEMPLATE_CODE = "content/sample/sequencing-library/1.0"
+    LIBRARY_MATERIAL_TEMPLATE_CODE = "material/sample/sequencing-library/1.0"
     SEQUENCING_RUN_TEMPLATE_BY_SUBTYPE = {
         "illumina": "data/sequencing_run/illumina/1.0",
         "ont": "data/sequencing_run/ont/1.0",
@@ -73,8 +73,8 @@ class BetaLabService(
     }
     LIBRARY_PLATE_TEMPLATE_CODE = "container/plate/sequencing-library-plate-96/1.0"
     EXTRACTION_TEMPLATE_BY_TYPE = {
-        "cfdna": "content/sample/cfdna/1.0",
-        "gdna": "content/sample/gdna/1.0",
+        "cfdna": "material/sample/cfdna/1.0",
+        "gdna": "material/sample/gdna/1.0",
     }
     LIB_PREP_QUEUE_BY_PLATFORM = {
         "ILMN": "ilmn_lib_prep",
diff --git a/bloom_lims/domain/execution_queue.py b/bloom_lims/domain/execution_queue.py
index 499603c..bdf0f6e 100644
--- a/bloom_lims/domain/execution_queue.py
+++ b/bloom_lims/domain/execution_queue.py
@@ -130,7 +130,7 @@ class ExecutionQueueService:
             "dispatch_priority": 100,
             "subject_template_codes": [
                 "container/tube/tube-generic-10ml/1.0",
-                "content/specimen/blood-whole/1.0",
+                "material/specimen/blood-whole/1.0",
             ],
             "required_worker_capabilities": ["wetlab.extraction"],
         },
@@ -139,7 +139,7 @@ class ExecutionQueueService:
             "dispatch_priority": 90,
             "subject_template_codes": [
                 "container/tube/tube-generic-10ml/1.0",
-                "content/specimen/blood-whole/1.0",
+                "material/specimen/blood-whole/1.0",
             ],
             "required_worker_capabilities": ["wetlab.extraction"],
         },
@@ -147,8 +147,8 @@ class ExecutionQueueService:
             "display_name": "Post-Extract QC",
             "dispatch_priority": 100,
             "subject_template_codes": [
-                "content/sample/cfdna/1.0",
-                "content/sample/gdna/1.0",
+                "material/sample/cfdna/1.0",
+                "material/sample/gdna/1.0",
             ],
             "required_worker_capabilities": ["wetlab.post_extract_qc"],
         },
@@ -156,8 +156,8 @@ class ExecutionQueueService:
             "display_name": "Illumina Library Prep",
             "dispatch_priority": 100,
             "subject_template_codes": [
-                "content/sample/cfdna/1.0",
-                "content/sample/gdna/1.0",
+                "material/sample/cfdna/1.0",
+                "material/sample/gdna/1.0",
             ],
             "required_worker_capabilities": ["wetlab.library_prep", "platform.ILMN"],
         },
@@ -165,7 +165,7 @@ class ExecutionQueueService:
             "display_name": "Illumina Library QC",
             "dispatch_priority": 100,
             "subject_template_codes": [
-                "content/sample/sequencing-library/1.0",
+                "material/sample/sequencing-library/1.0",
             ],
             "required_worker_capabilities": ["wetlab.library_qc", "platform.ILMN"],
         },
@@ -173,8 +173,8 @@ class ExecutionQueueService:
             "display_name": "ONT Library Prep",
             "dispatch_priority": 100,
             "subject_template_codes": [
-                "content/sample/cfdna/1.0",
-                "content/sample/gdna/1.0",
+                "material/sample/cfdna/1.0",
+                "material/sample/gdna/1.0",
             ],
             "required_worker_capabilities": ["wetlab.library_prep", "platform.ONT"],
         },
@@ -183,7 +183,7 @@ class ExecutionQueueService:
             "dispatch_priority": 100,
             "subject_template_codes": [
                 "data/operation/library-prep/1.0",
-                "content/sample/sequencing-library/1.0",
+                "material/sample/sequencing-library/1.0",
             ],
             "required_worker_capabilities": ["wetlab.pooling", "platform.ILMN"],
         },
@@ -192,28 +192,28 @@ class ExecutionQueueService:
             "dispatch_priority": 100,
             "subject_template_codes": [
                 "data/operation/library-prep/1.0",
-                "content/sample/sequencing-library/1.0",
+                "material/sample/sequencing-library/1.0",
             ],
             "required_worker_capabilities": ["wetlab.pooling", "platform.ONT"],
         },
         "ilmn_start_seq_run": {
             "display_name": "Illumina Start Run",
             "dispatch_priority": 100,
-            "subject_template_codes": ["content/pool/sequencing-library/1.0"],
+            "subject_template_codes": ["material/pool/sequencing-library/1.0"],
             "required_worker_capabilities": ["wetlab.run_start", "platform.ILMN"],
         },
         "ont_start_seq_run": {
             "display_name": "ONT Start Run",
             "dispatch_priority": 100,
-            "subject_template_codes": ["content/pool/sequencing-library/1.0"],
+            "subject_template_codes": ["material/pool/sequencing-library/1.0"],
             "required_worker_capabilities": ["wetlab.run_start", "platform.ONT"],
         },
         "post_extract_exception": {
             "display_name": "Post-Extract QC Exception",
             "dispatch_priority": 10,
             "subject_template_codes": [
-                "content/sample/cfdna/1.0",
-                "content/sample/gdna/1.0",
+                "material/sample/cfdna/1.0",
+                "material/sample/gdna/1.0",
             ],
             "required_worker_capabilities": ["wetlab.exception_review"],
         },
@@ -221,7 +221,7 @@ class ExecutionQueueService:
             "display_name": "Illumina Library QC Exception",
             "dispatch_priority": 10,
             "subject_template_codes": [
-                "content/sample/sequencing-library/1.0",
+                "material/sample/sequencing-library/1.0",
             ],
             "required_worker_capabilities": [
                 "wetlab.exception_review",
diff --git a/bloom_lims/domain/lab_actions.py b/bloom_lims/domain/lab_actions.py
index 99fcbdc..6adb276 100644
--- a/bloom_lims/domain/lab_actions.py
+++ b/bloom_lims/domain/lab_actions.py
@@ -40,10 +40,10 @@
 RUN_SET_TEMPLATE_CODE = "set/run-set/generic/1.01/"
 EXTRACTION_PLATE_TEMPLATE_CODE = "container/plate/fixed-plate-96/1.0/"
 LIBRARY_PLATE_TEMPLATE_CODE = "container/plate/sequencing-library-plate-96/1.0/"
-GDNA_TEMPLATE_CODE = "content/sample/gdna/1.0/"
-LIBRARY_CONTENT_TEMPLATE_CODE = "content/sample/sequencing-library/1.0/"
+GDNA_TEMPLATE_CODE = "material/sample/gdna/1.0/"
+LIBRARY_CONTENT_TEMPLATE_CODE = "material/sample/sequencing-library/1.0/"
 POOL_TUBE_TEMPLATE_CODE = "container/tube/tube-generic-10ml/1.0/"
-POOL_CONTENT_TEMPLATE_CODE = "content/pool/sequencing-library/1.0/"
+POOL_CONTENT_TEMPLATE_CODE = "material/pool/sequencing-library/1.0/"
 GDNA_QUANT_TEMPLATE_CODE = "data/quantification/gdna/1.0/"
 EXTRACTION_QC_TEMPLATE_CODE = "data/operation/extraction-qc/1.0/"
 SEQUENCED_LIBRARY_ASSIGNMENT_TEMPLATE_CODE = (
diff --git a/bloom_lims/schemas/beta_lab.py b/bloom_lims/schemas/beta_lab.py
index cf123ae..1e855ea 100644
--- a/bloom_lims/schemas/beta_lab.py
+++ b/bloom_lims/schemas/beta_lab.py
@@ -174,7 +174,7 @@ def validate_context(self) -> "AtlasFulfillmentContext":
 
 
 class BetaAcceptedMaterialCreateRequest(BaseModel):
-    specimen_template_code: str = Field(default="content/specimen/blood-whole/1.0")
+    specimen_template_code: str = Field(default="material/specimen/blood-whole/1.0")
     specimen_name: str | None = None
     container_euid: str | None = None
     container_template_code: str = Field(default="container/tube/tube-generic-10ml/1.0")
diff --git a/bloom_lims/schemas/external_specimens.py b/bloom_lims/schemas/external_specimens.py
index df3a009..041c7be 100644
--- a/bloom_lims/schemas/external_specimens.py
+++ b/bloom_lims/schemas/external_specimens.py
@@ -20,7 +20,7 @@ class AtlasReferences(BaseModel):
 
 
 class ExternalSpecimenCreateRequest(BaseModel):
-    specimen_template_code: str = Field(default="content/specimen/generic/1.0")
+    specimen_template_code: str = Field(default="material/specimen/generic/1.0")
     specimen_name: str | None = None
     container_euid: str | None = None
     container_template_code: str = Field(default="container/tube/generic/1.0")
diff --git a/config/tapdb_templates/bloom/templates.json b/config/tapdb_templates/bloom/templates.json
index be5aabf..77d6319 100644
--- a/config/tapdb_templates/bloom/templates.json
+++ b/config/tapdb_templates/bloom/templates.json
@@ -4,7 +4,7 @@
     {
       "name": "Claim Material In Queue",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "claim_material_in_queue",
       "version": "1.0",
@@ -27,7 +27,7 @@
     {
       "name": "Consume Material",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "consume_material",
       "version": "1.0",
@@ -50,7 +50,7 @@
     {
       "name": "Create Empty Tube",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "create_empty_tube",
       "version": "1.0",
@@ -73,7 +73,7 @@
     {
       "name": "Create Extraction",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "create_extraction",
       "version": "1.0",
@@ -96,7 +96,7 @@
     {
       "name": "Create Library Prep",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "create_library_prep",
       "version": "1.0",
@@ -119,7 +119,7 @@
     {
       "name": "Create Pool",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "create_pool",
       "version": "1.0",
@@ -142,7 +142,7 @@
     {
       "name": "Record Library QC",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "record_library_qc",
       "version": "1.0",
@@ -165,7 +165,7 @@
     {
       "name": "Create Run",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "create_run",
       "version": "1.0",
@@ -188,7 +188,7 @@
     {
       "name": "Move Material To Queue",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "move_material_to_queue",
       "version": "1.0",
@@ -211,7 +211,7 @@
     {
       "name": "Record Post Extract QC",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "record_post_extract_qc",
       "version": "1.0",
@@ -234,7 +234,7 @@
     {
       "name": "Register Accepted Material",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "register_accepted_material",
       "version": "1.0",
@@ -257,7 +257,7 @@
     {
       "name": "Release Claim",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "release_claim",
       "version": "1.0",
@@ -280,7 +280,7 @@
     {
       "name": "Release Reservation",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "release_reservation",
       "version": "1.0",
@@ -303,7 +303,7 @@
     {
       "name": "Reserve Material",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "reserve_material",
       "version": "1.0",
@@ -326,7 +326,7 @@
     {
       "name": "Update Specimen",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "update_specimen",
       "version": "1.0",
@@ -349,7 +349,7 @@
     {
       "name": "Update Tube",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "beta_lab",
       "subtype": "update_tube",
       "version": "1.0",
@@ -372,7 +372,7 @@
     {
       "name": "action/core/add-relationships/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "core",
       "subtype": "add-relationships",
       "version": "1.0",
@@ -408,7 +408,7 @@
     {
       "name": "action/core/create-subject-and-anchor/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "core",
       "subtype": "create-subject-and-anchor",
       "version": "1.0",
@@ -444,7 +444,7 @@
     {
       "name": "action/core/print_barcode_label/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "core",
       "subtype": "print_barcode_label",
       "version": "1.0",
@@ -488,7 +488,7 @@
     {
       "name": "action/core/set_object_status/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "core",
       "subtype": "set_object_status",
       "version": "1.0",
@@ -528,7 +528,7 @@
     {
       "name": "action/data/log-temperature/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "data",
       "subtype": "log-temperature",
       "version": "1.0",
@@ -571,7 +571,7 @@
     {
       "name": "action/data/record_cfdna_quant_outcome/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "data",
       "subtype": "record_cfdna_quant_outcome",
       "version": "1.0",
@@ -614,7 +614,7 @@
     {
       "name": "action/equipment/add-container-to/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "equipment",
       "subtype": "add-container-to",
       "version": "1.0",
@@ -661,7 +661,7 @@
     {
       "name": "action/equipment/download-inventory-tsv/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "equipment",
       "subtype": "download-inventory-tsv",
       "version": "1.0",
@@ -707,7 +707,7 @@
     {
       "name": "action/equipment/log-temperature/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "equipment",
       "subtype": "log-temperature",
       "version": "1.0",
@@ -760,7 +760,7 @@
     {
       "name": "action/equipment/remove-container-from/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "equipment",
       "subtype": "remove-container-from",
       "version": "1.0",
@@ -806,7 +806,7 @@
     {
       "name": "Cancel Subject Execution",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "cancel_subject_execution",
       "version": "1.0",
@@ -829,7 +829,7 @@
     {
       "name": "Claim Queue Item",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "claim_queue_item",
       "version": "1.0",
@@ -852,7 +852,7 @@
     {
       "name": "Complete Queue Execution",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "complete_queue_execution",
       "version": "1.0",
@@ -875,7 +875,7 @@
     {
       "name": "Expire Queue Lease",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "expire_queue_lease",
       "version": "1.0",
@@ -898,7 +898,7 @@
     {
       "name": "Fail Queue Execution",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "fail_queue_execution",
       "version": "1.0",
@@ -921,7 +921,7 @@
     {
       "name": "Heartbeat Worker",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "heartbeat_worker",
       "version": "1.0",
@@ -944,7 +944,7 @@
     {
       "name": "Place Execution Hold",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "place_execution_hold",
       "version": "1.0",
@@ -967,7 +967,7 @@
     {
       "name": "Register Worker",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "register_worker",
       "version": "1.0",
@@ -990,7 +990,7 @@
     {
       "name": "Release Execution Hold",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "release_execution_hold",
       "version": "1.0",
@@ -1013,7 +1013,7 @@
     {
       "name": "Release Queue Lease",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "release_queue_lease",
       "version": "1.0",
@@ -1036,7 +1036,7 @@
     {
       "name": "Renew Queue Lease",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "renew_queue_lease",
       "version": "1.0",
@@ -1059,7 +1059,7 @@
     {
       "name": "Requeue Subject",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "execution_queue",
       "subtype": "requeue_subject",
       "version": "1.0",
@@ -1082,7 +1082,7 @@
     {
       "name": "action/file/download_file/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "file",
       "subtype": "download_file",
       "version": "1.0",
@@ -1118,7 +1118,7 @@
     {
       "name": "action/move-queues/move-among-ay-top-queues/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "move-queues",
       "subtype": "move-among-ay-top-queues",
       "version": "1.0",
@@ -1162,7 +1162,7 @@
     {
       "name": "action/object/set-child-object/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "object",
       "subtype": "set-child-object",
       "version": "1.0",
@@ -1210,7 +1210,7 @@
     {
       "name": "action/plate/download_plate_map/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "plate",
       "subtype": "download_plate_map",
       "version": "1.0",
@@ -1255,7 +1255,7 @@
     {
       "name": "action/plate/stamp_plates_into_plate/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "plate",
       "subtype": "stamp_plates_into_plate",
       "version": "1.0",
@@ -1313,7 +1313,7 @@
     {
       "name": "action/plate/stamp_plates_into_plate__extraction_plate_filled/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "plate",
       "subtype": "stamp_plates_into_plate__extraction_plate_filled",
       "version": "1.0",
@@ -1371,7 +1371,7 @@
     {
       "name": "action/pool/create-pool-from-containers/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "pool",
       "subtype": "create-pool-from-containers",
       "version": "1.0",
@@ -1438,7 +1438,7 @@
     {
       "name": "action/pool/create_pool_from_containers__extraction_plate_filled/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "pool",
       "subtype": "create_pool_from_containers__extraction_plate_filled",
       "version": "1.0",
@@ -1505,7 +1505,7 @@
     {
       "name": "action/workflow/destroy_specimen_containers/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow",
       "subtype": "destroy_specimen_containers",
       "version": "1.0",
@@ -1559,7 +1559,7 @@
     {
       "name": "action/workflow_step_analysis/download_quant_data/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_analysis",
       "subtype": "download_quant_data",
       "version": "1.0",
@@ -1605,7 +1605,7 @@
     {
       "name": "action/workflow_step_destroy/complete_specimen_destroy/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_destroy",
       "subtype": "complete_specimen_destroy",
       "version": "1.0",
@@ -1649,7 +1649,7 @@
     {
       "name": "action/workflow_step_extraction/cfdna_post_extraction_quant/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_extraction",
       "subtype": "cfdna_post_extraction_quant",
       "version": "1.0",
@@ -1711,7 +1711,7 @@
     {
       "name": "action/workflow_step_plate_operations/cfdna_quant/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_plate_operations",
       "subtype": "cfdna_quant",
       "version": "1.0",
@@ -1773,7 +1773,7 @@
     {
       "name": "action/workflow_step_plate_operations/stamp_copy_plate/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_plate_operations",
       "subtype": "stamp_copy_plate",
       "version": "1.0",
@@ -1826,7 +1826,7 @@
     {
       "name": "action/workflow_step_queue/add-gdna-to-gdna-normalization-queue/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "add-gdna-to-gdna-normalization-queue",
       "version": "1.0",
@@ -1869,7 +1869,7 @@
     {
       "name": "action/workflow_step_queue/add-to-blood-gdna-extraction-queue/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "add-to-blood-gdna-extraction-queue",
       "version": "1.0",
@@ -1912,7 +1912,7 @@
     {
       "name": "action/workflow_step_queue/add-to-buccal-gdna-extraction-queue/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "add-to-buccal-gdna-extraction-queue",
       "version": "1.0",
@@ -1955,7 +1955,7 @@
     {
       "name": "action/workflow_step_queue/create_test_req_and_link_child_workflow_step/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "create_test_req_and_link_child_workflow_step",
       "version": "1.0",
@@ -2019,7 +2019,7 @@
     {
       "name": "action/workflow_step_queue/existing-plate-fill-auto/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "existing-plate-fill-auto",
       "version": "1.0",
@@ -2061,7 +2061,7 @@
     {
       "name": "action/workflow_step_queue/existing-plate-fill-directed/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "existing-plate-fill-directed",
       "version": "1.0",
@@ -2103,7 +2103,7 @@
     {
       "name": "action/workflow_step_queue/fill_plate_directed/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "fill_plate_directed",
       "version": "1.0",
@@ -2152,7 +2152,7 @@
     {
       "name": "action/workflow_step_queue/fill_plate_undirected/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "fill_plate_undirected",
       "version": "1.0",
@@ -2205,7 +2205,7 @@
     {
       "name": "action/workflow_step_queue/link_tubes_auto/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "link_tubes_auto",
       "version": "1.0",
@@ -2276,7 +2276,7 @@
     {
       "name": "action/workflow_step_queue/plate-create-fill-auto/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "plate-create-fill-auto",
       "version": "1.0",
@@ -2318,7 +2318,7 @@
     {
       "name": "action/workflow_step_queue/plate-create-fill-directed/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "plate-create-fill-directed",
       "version": "1.0",
@@ -2360,7 +2360,7 @@
     {
       "name": "action/workflow_step_queue/save-quant-data/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "save-quant-data",
       "version": "1.0",
@@ -2402,7 +2402,7 @@
     {
       "name": "action/workflow_step_queue/ycreate_test_req_and_link_child_workflow_step/1.0",
       "polymorphic_discriminator": "action_template",
-      "category": "BAC",
+      "category": "action",
       "type": "workflow_step_queue",
       "subtype": "ycreate_test_req_and_link_child_workflow_step",
       "version": "1.0",
@@ -2464,7 +2464,7 @@
     {
       "name": "Bloom Authenticated User",
       "polymorphic_discriminator": "actor_template",
-      "category": "BAR",
+      "category": "actor",
       "type": "generic",
       "subtype": "bloom-user",
       "version": "1.0",
@@ -2475,10 +2475,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Bloom Authenticated User",
         "expected_inputs": [],
@@ -2497,7 +2497,7 @@
     {
       "name": "Patient",
       "polymorphic_discriminator": "actor_template",
-      "category": "BAR",
+      "category": "actor",
       "type": "generic",
       "subtype": "patient",
       "version": "1.0",
@@ -2508,10 +2508,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Patient",
         "expected_inputs": [],
@@ -2534,7 +2534,7 @@
     {
       "name": "Clinician",
       "polymorphic_discriminator": "actor_template",
-      "category": "BAR",
+      "category": "actor",
       "type": "generic",
       "subtype": "physician",
       "version": "1.0",
@@ -2545,10 +2545,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -2581,7 +2581,7 @@
     {
       "name": "Execution System Worker",
       "polymorphic_discriminator": "actor_template",
-      "category": "BAR",
+      "category": "actor",
       "type": "system",
       "subtype": "worker",
       "version": "1.0",
@@ -2592,9 +2592,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Execution System Worker",
         "expected_inputs": [],
@@ -2628,7 +2628,7 @@
     {
       "name": "Bloom User",
       "polymorphic_discriminator": "generic_template",
-      "category": "BAR",
+      "category": "actor",
       "type": "user",
       "subtype": "bloom-user",
       "version": "1.0",
@@ -2653,10 +2653,10 @@
             "group_order": "1",
             "group_name": "Core Actions",
             "actions": {
-              "BAC/core/add-relationships/1.0": {},
-              "BAC/core/create-subject-and-anchor/1.0": {},
-              "BAC/core/print_barcode_label/1.0": {},
-              "BAC/core/set_object_status/1.0": {}
+              "action/core/add-relationships/1.0": {},
+              "action/core/create-subject-and-anchor/1.0": {},
+              "action/core/print_barcode_label/1.0": {},
+              "action/core/set_object_status/1.0": {}
             }
           }
         },
@@ -2667,9 +2667,9 @@
     {
       "name": "Bloom User API Token Usage Log",
       "polymorphic_discriminator": "generic_template",
-      "category": "BBX",
-      "type": "auth",
-      "subtype": "user-api-token-usage-log",
+      "category": "auth",
+      "type": "user-api-token-usage-log",
+      "subtype": "generic",
       "version": "1.0",
       "instance_prefix": "BBX",
       "instance_polymorphic_identity": "generic_instance",
@@ -2684,9 +2684,9 @@
     {
       "name": "Bloom User API Token",
       "polymorphic_discriminator": "generic_template",
-      "category": "BBX",
-      "type": "auth",
-      "subtype": "user-api-token",
+      "category": "auth",
+      "type": "user-api-token",
+      "subtype": "generic",
       "version": "1.0",
       "instance_prefix": "BBX",
       "instance_polymorphic_identity": "generic_instance",
@@ -2701,7 +2701,7 @@
     {
       "name": "Generic External Object Link",
       "polymorphic_discriminator": "generic_template",
-      "category": "BGX",
+      "category": "generic",
       "type": "generic",
       "subtype": "external_object_link",
       "version": "1.0",
@@ -2725,9 +2725,9 @@
     {
       "name": "Bloom User Group Membership",
       "polymorphic_discriminator": "generic_template",
-      "category": "BBX",
-      "type": "auth",
-      "subtype": "user-group-membership",
+      "category": "auth",
+      "type": "user-group-membership",
+      "subtype": "generic",
       "version": "1.0",
       "instance_prefix": "BBX",
       "instance_polymorphic_identity": "generic_instance",
@@ -2742,9 +2742,9 @@
     {
       "name": "Bloom User Group",
       "polymorphic_discriminator": "generic_template",
-      "category": "BBX",
-      "type": "auth",
-      "subtype": "user-group",
+      "category": "auth",
+      "type": "user-group",
+      "subtype": "generic",
       "version": "1.0",
       "instance_prefix": "BBX",
       "instance_polymorphic_identity": "generic_instance",
@@ -2759,7 +2759,7 @@
     {
       "name": "24 fixed well plate",
       "polymorphic_discriminator": "container_template",
-      "category": "BCP",
+      "category": "container",
       "type": "plate",
       "subtype": "fixed-plate-24",
       "version": "1.0",
@@ -2770,12 +2770,12 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "download_plate_map": "BAC/plate/download_plate_map/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0",
-          "stamp_plates_into_plate": "BAC/plate/stamp_plates_into_plate/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "download_plate_map": "action/plate/download_plate_map/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0",
+          "stamp_plates_into_plate": "action/plate/stamp_plates_into_plate/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -3300,7 +3300,7 @@
     {
       "name": "96 well fixed plate",
       "polymorphic_discriminator": "container_template",
-      "category": "BCP",
+      "category": "container",
       "type": "plate",
       "subtype": "fixed-plate-96",
       "version": "1.0",
@@ -3311,12 +3311,12 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "download_plate_map": "BAC/plate/download_plate_map/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0",
-          "stamp_plates_into_plate": "BAC/plate/stamp_plates_into_plate/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "download_plate_map": "action/plate/download_plate_map/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0",
+          "stamp_plates_into_plate": "action/plate/stamp_plates_into_plate/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -4934,7 +4934,7 @@
     {
       "name": "4 position Rack",
       "polymorphic_discriminator": "container_template",
-      "category": "BCR",
+      "category": "container",
       "type": "rack",
       "subtype": "tube-rack-4-empty",
       "version": "1.0",
@@ -4945,10 +4945,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -4987,7 +4987,7 @@
     {
       "name": "4 position Rack",
       "polymorphic_discriminator": "container_template",
-      "category": "BCR",
+      "category": "container",
       "type": "rack",
       "subtype": "tube-rack-generic",
       "version": "1.0",
@@ -4998,10 +4998,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5094,7 +5094,7 @@
     {
       "name": "Shelf",
       "polymorphic_discriminator": "container_template",
-      "category": "BCR",
+      "category": "container",
       "type": "shelf",
       "subtype": "generic",
       "version": "1.0",
@@ -5105,11 +5105,11 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_container_to": "BAC/equipment/add-container-to/1.0",
-          "download_inventory_tsv": "BAC/equipment/download-inventory-tsv/1.0",
-          "log_temperature": "BAC/equipment/log-temperature/1.0",
-          "remove_container_from": "BAC/equipment/remove-container-from/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_container_to": "action/equipment/add-container-to/1.0",
+          "download_inventory_tsv": "action/equipment/download-inventory-tsv/1.0",
+          "log_temperature": "action/equipment/log-temperature/1.0",
+          "remove_container_from": "action/equipment/remove-container-from/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5150,7 +5150,7 @@
     {
       "name": "10ml glass tube",
       "polymorphic_discriminator": "container_template",
-      "category": "BCT",
+      "category": "container",
       "type": "tube",
       "subtype": "tube-10ml-glass",
       "version": "1.0",
@@ -5161,10 +5161,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5197,7 +5197,7 @@
           "name": "10ml glass tube"
         },
         "valid_content": [
-          "content/.*"
+          "material/.*"
         ],
         "valid_parents": [],
         "semantic_category": "container"
@@ -5206,7 +5206,7 @@
     {
       "name": "1.5ml eppi tube",
       "polymorphic_discriminator": "container_template",
-      "category": "BCT",
+      "category": "container",
       "type": "tube",
       "subtype": "tube-eppi-1.5ml",
       "version": "1.0",
@@ -5217,10 +5217,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5253,7 +5253,7 @@
           "name": "1.5ml eppi tube"
         },
         "valid_content": [
-          "content/.*"
+          "material/.*"
         ],
         "valid_parents": [],
         "semantic_category": "container"
@@ -5262,7 +5262,7 @@
     {
       "name": "Generic 10ml tube",
       "polymorphic_discriminator": "container_template",
-      "category": "BCT",
+      "category": "container",
       "type": "tube",
       "subtype": "tube-generic-10ml",
       "version": "1.0",
@@ -5273,10 +5273,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5309,7 +5309,7 @@
           "name": "10ml tube generic"
         },
         "valid_content": [
-          "content/.*"
+          "material/.*"
         ],
         "valid_parents": [],
         "semantic_category": "container"
@@ -5318,7 +5318,7 @@
     {
       "name": "strek 10ml",
       "polymorphic_discriminator": "container_template",
-      "category": "BCT",
+      "category": "container",
       "type": "tube",
       "subtype": "tube-strek-10ml",
       "version": "1.0",
@@ -5329,10 +5329,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5366,7 +5366,7 @@
         },
         "singleton": "0",
         "valid_content": [
-          "content/.*"
+          "material/.*"
         ],
         "valid_parents": [],
         "semantic_category": "container"
@@ -5375,7 +5375,7 @@
     {
       "name": "Mawi DNA Technologies - ISD-T-250 - iSWAB DNA Collection Tube - Buccal",
       "polymorphic_discriminator": "container_template",
-      "category": "BCT",
+      "category": "container",
       "type": "tube",
       "subtype": "mawi-isd-t-250-iswab-dna-collection-tube-buccal",
       "version": "1.0",
@@ -5386,10 +5386,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5426,7 +5426,7 @@
         },
         "singleton": "0",
         "valid_content": [
-          "content/.*"
+          "material/.*"
         ],
         "valid_parents": [],
         "semantic_category": "container"
@@ -5435,7 +5435,7 @@
     {
       "name": "plate well - fixed",
       "polymorphic_discriminator": "container_template",
-      "category": "BCW",
+      "category": "container",
       "type": "well",
       "subtype": "fixed-plate-well",
       "version": "1.0",
@@ -5446,7 +5446,7 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5479,7 +5479,7 @@
         },
         "singleton": "0",
         "valid_content": [
-          "content/.*"
+          "material/.*"
         ],
         "valid_parents": [
           "container/plate/fixed-plate.*?/.*?"
@@ -5490,7 +5490,7 @@
     {
       "name": "giab NA12878",
       "polymorphic_discriminator": "content_template",
-      "category": "BNK",
+      "category": "material",
       "type": "control",
       "subtype": "giab-HG001",
       "version": "1.0",
@@ -5501,10 +5501,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5534,7 +5534,7 @@
     {
       "name": "giab NA24385",
       "polymorphic_discriminator": "content_template",
-      "category": "BNK",
+      "category": "material",
       "type": "control",
       "subtype": "giab-HG002",
       "version": "1.0",
@@ -5545,10 +5545,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5578,7 +5578,7 @@
     {
       "name": "synthetic-cfdna",
       "polymorphic_discriminator": "content_template",
-      "category": "BNK",
+      "category": "material",
       "type": "control",
       "subtype": "synthetic-cfdna",
       "version": "1.0",
@@ -5589,10 +5589,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5622,7 +5622,7 @@
     {
       "name": "NTC - water",
       "polymorphic_discriminator": "content_template",
-      "category": "BNK",
+      "category": "material",
       "type": "control",
       "subtype": "water-ntc",
       "version": "1.0",
@@ -5633,10 +5633,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -5666,7 +5666,7 @@
     {
       "name": "Pool of Contents",
       "polymorphic_discriminator": "content_template",
-      "category": "BNP",
+      "category": "material",
       "type": "pool",
       "subtype": "generic",
       "version": "1.0",
@@ -5702,7 +5702,7 @@
     {
       "name": "Novaseq sequencing kit",
       "polymorphic_discriminator": "content_template",
-      "category": "BNR",
+      "category": "material",
       "type": "reagent",
       "subtype": "ILMN-nova-seq-kit",
       "version": "1.0",
@@ -5745,7 +5745,7 @@
     {
       "name": "idt probes for rare mendelian disease, v1.0",
       "polymorphic_discriminator": "content_template",
-      "category": "BNR",
+      "category": "material",
       "type": "reagent",
       "subtype": "idt-probes-rare-mendelian",
       "version": "1.0",
@@ -5788,7 +5788,7 @@
     {
       "name": "NaOH",
       "polymorphic_discriminator": "content_template",
-      "category": "BNR",
+      "category": "material",
       "type": "reagent",
       "subtype": "naoh",
       "version": "1.0",
@@ -5832,7 +5832,7 @@
     {
       "name": "plasma (whole blood)",
       "polymorphic_discriminator": "content_template",
-      "category": "BNB",
+      "category": "material",
       "type": "sample",
       "subtype": "blood-plasma",
       "version": "1.0",
@@ -5870,7 +5870,7 @@
     {
       "name": "cell free DNA ",
       "polymorphic_discriminator": "content_template",
-      "category": "BNC",
+      "category": "material",
       "type": "sample",
       "subtype": "cfdna",
       "version": "1.0",
@@ -5908,7 +5908,7 @@
     {
       "name": "genomic DNA",
       "polymorphic_discriminator": "content_template",
-      "category": "BNG",
+      "category": "material",
       "type": "sample",
       "subtype": "gdna",
       "version": "1.0",
@@ -5946,7 +5946,7 @@
     {
       "name": "Whole Blood",
       "polymorphic_discriminator": "content_template",
-      "category": "BNB",
+      "category": "material",
       "type": "specimen",
       "subtype": "blood-whole",
       "version": "1.0",
@@ -5984,7 +5984,7 @@
     {
       "name": "Buccal Swab",
       "polymorphic_discriminator": "content_template",
-      "category": "BNS",
+      "category": "material",
       "type": "specimen",
       "subtype": "buccal-swab",
       "version": "1.0",
@@ -6022,7 +6022,7 @@
     {
       "name": "FFPE Block",
       "polymorphic_discriminator": "content_template",
-      "category": "BNF",
+      "category": "material",
       "type": "specimen",
       "subtype": "ffpe-block",
       "version": "1.0",
@@ -6060,7 +6060,7 @@
     {
       "name": "FFPE Slides",
       "polymorphic_discriminator": "content_template",
-      "category": "BNF",
+      "category": "material",
       "type": "specimen",
       "subtype": "ffpe-slice",
       "version": "1.0",
@@ -6098,7 +6098,7 @@
     {
       "name": "Execution Dead Letter Record",
       "polymorphic_discriminator": "data_template",
-      "category": "BDT",
+      "category": "data",
       "type": "execution",
       "subtype": "dead_letter",
       "version": "1.0",
@@ -6109,9 +6109,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Execution Dead Letter Record",
         "expected_inputs": [],
@@ -6137,7 +6137,7 @@
     {
       "name": "Execution Attempt Record",
       "polymorphic_discriminator": "data_template",
-      "category": "BDT",
+      "category": "data",
       "type": "execution",
       "subtype": "execution_record",
       "version": "1.0",
@@ -6148,9 +6148,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Execution Attempt Record",
         "expected_inputs": [],
@@ -6190,7 +6190,7 @@
     {
       "name": "Execution Hold",
       "polymorphic_discriminator": "data_template",
-      "category": "BDT",
+      "category": "data",
       "type": "execution",
       "subtype": "hold",
       "version": "1.0",
@@ -6201,9 +6201,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Execution Hold",
         "expected_inputs": [],
@@ -6227,7 +6227,7 @@
     {
       "name": "Execution Queue Definition",
       "polymorphic_discriminator": "data_template",
-      "category": "BDT",
+      "category": "data",
       "type": "execution",
       "subtype": "queue",
       "version": "1.0",
@@ -6238,10 +6238,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Execution Queue Definition",
         "expected_inputs": [],
@@ -6291,7 +6291,7 @@
     {
       "name": "Execution Queue Lease",
       "polymorphic_discriminator": "data_template",
-      "category": "BDT",
+      "category": "data",
       "type": "execution",
       "subtype": "queue_lease",
       "version": "1.0",
@@ -6302,9 +6302,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Execution Queue Lease",
         "expected_inputs": [],
@@ -6335,7 +6335,7 @@
     {
       "name": "Generic Data Record",
       "polymorphic_discriminator": "data_template",
-      "category": "BD",
+      "category": "data",
       "type": "generic",
       "subtype": "generic",
       "version": "1.0",
@@ -6346,9 +6346,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Generic data record",
         "expected_inputs": [],
@@ -6365,7 +6365,7 @@
     {
       "name": "DNA Quant Data",
       "polymorphic_discriminator": "data_template",
-      "category": "BDQ",
+      "category": "data",
       "type": "generic",
       "subtype": "gdna-quantification",
       "version": "1.0",
@@ -6376,11 +6376,11 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "record_cfdna_quant_outcome": "BAC/data/record_cfdna_quant_outcome/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "record_cfdna_quant_outcome": "action/data/record_cfdna_quant_outcome/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -6408,7 +6408,7 @@
     {
       "name": "Temperature Log Data",
       "polymorphic_discriminator": "data_template",
-      "category": "BDC",
+      "category": "data",
       "type": "generic",
       "subtype": "temperature-log",
       "version": "1.0",
@@ -6445,7 +6445,7 @@
     {
       "name": "Wet-Lab Library Prep Output",
       "polymorphic_discriminator": "data_template",
-      "category": "BDP",
+      "category": "data",
       "type": "wetlab",
       "subtype": "library_prep_output",
       "version": "1.0",
@@ -6456,10 +6456,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Wet-Lab Library Prep Output",
         "expected_inputs": [],
@@ -6478,7 +6478,7 @@
     {
       "name": "Illumina Sequencing Run",
       "polymorphic_discriminator": "data_template",
-      "category": "BRM",
+      "category": "data",
       "type": "sequencing_run",
       "subtype": "illumina",
       "version": "1.0",
@@ -6489,9 +6489,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Sequencing run executed on an Illumina instrument.",
         "expected_inputs": [],
@@ -6516,7 +6516,7 @@
     {
       "name": "ONT Sequencing Run",
       "polymorphic_discriminator": "data_template",
-      "category": "BRN",
+      "category": "data",
       "type": "sequencing_run",
       "subtype": "ont",
       "version": "1.0",
@@ -6527,9 +6527,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Sequencing run executed on an Oxford Nanopore instrument.",
         "expected_inputs": [],
@@ -6554,7 +6554,7 @@
     {
       "name": "Ultima Sequencing Run",
       "polymorphic_discriminator": "data_template",
-      "category": "BRT",
+      "category": "data",
       "type": "sequencing_run",
       "subtype": "ultima",
       "version": "1.0",
@@ -6565,9 +6565,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Sequencing run executed on an Ultima instrument.",
         "expected_inputs": [],
@@ -6592,7 +6592,7 @@
     {
       "name": "CompleteGenomics Sequencing Run",
       "polymorphic_discriminator": "data_template",
-      "category": "BRC",
+      "category": "data",
       "type": "sequencing_run",
       "subtype": "completegenomics",
       "version": "1.0",
@@ -6603,9 +6603,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Sequencing run executed on a Complete Genomics instrument.",
         "expected_inputs": [],
@@ -6630,7 +6630,7 @@
     {
       "name": "PacBio Sequencing Run",
       "polymorphic_discriminator": "data_template",
-      "category": "BRP",
+      "category": "data",
       "type": "sequencing_run",
       "subtype": "pacbio",
       "version": "1.0",
@@ -6641,9 +6641,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Sequencing run executed on a PacBio instrument.",
         "expected_inputs": [],
@@ -6668,7 +6668,7 @@
     {
       "name": "-20C Freezer",
       "polymorphic_discriminator": "equipment_template",
-      "category": "BEQ",
+      "category": "equipment",
       "type": "freezer",
       "subtype": "freezer-m20c",
       "version": "1.0",
@@ -6679,14 +6679,14 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_container_to": "BAC/equipment/add-container-to/1.0",
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "download_inventory_tsv": "BAC/equipment/download-inventory-tsv/1.0",
-          "log_temperature": "BAC/equipment/log-temperature/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "remove_container_from": "BAC/equipment/remove-container-from/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_container_to": "action/equipment/add-container-to/1.0",
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "download_inventory_tsv": "action/equipment/download-inventory-tsv/1.0",
+          "log_temperature": "action/equipment/log-temperature/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "remove_container_from": "action/equipment/remove-container-from/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -6706,7 +6706,7 @@
             "relationship_type": "contains",
             "child_templates": [
               {
-                "template_code": "BCR/shelf/generic/1.0",
+                "template_code": "container/shelf/generic/1.0",
                 "json_addl": {
                   "cont_address": {
                     "capacity": "10",
@@ -6719,7 +6719,7 @@
                 }
               },
               {
-                "template_code": "BCR/shelf/generic/1.0",
+                "template_code": "container/shelf/generic/1.0",
                 "json_addl": {
                   "cont_address": {
                     "capacity": "10",
@@ -6750,7 +6750,7 @@
     {
       "name": "-80C Freezer.",
       "polymorphic_discriminator": "equipment_template",
-      "category": "BEQ",
+      "category": "equipment",
       "type": "freezer",
       "subtype": "freezer-m80c",
       "version": "1.0",
@@ -6761,14 +6761,14 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_container_to": "BAC/equipment/add-container-to/1.0",
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "download_inventory_tsv": "BAC/equipment/download-inventory-tsv/1.0",
-          "log_temperature": "BAC/equipment/log-temperature/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "remove_container_from": "BAC/equipment/remove-container-from/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_container_to": "action/equipment/add-container-to/1.0",
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "download_inventory_tsv": "action/equipment/download-inventory-tsv/1.0",
+          "log_temperature": "action/equipment/log-temperature/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "remove_container_from": "action/equipment/remove-container-from/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -6788,7 +6788,7 @@
             "relationship_type": "contains",
             "child_templates": [
               {
-                "template_code": "BCR/shelf/generic/1.0",
+                "template_code": "container/shelf/generic/1.0",
                 "json_addl": {
                   "cont_address": {
                     "capacity": "10",
@@ -6801,7 +6801,7 @@
                 }
               },
               {
-                "template_code": "BCR/shelf/generic/1.0",
+                "template_code": "container/shelf/generic/1.0",
                 "json_addl": {
                   "cont_address": {
                     "capacity": "10",
@@ -6814,7 +6814,7 @@
                 }
               },
               {
-                "template_code": "BCR/shelf/generic/1.0",
+                "template_code": "container/shelf/generic/1.0",
                 "json_addl": {
                   "cont_address": {
                     "capacity": "10",
@@ -6827,7 +6827,7 @@
                 }
               },
               {
-                "template_code": "BCR/shelf/generic/1.0",
+                "template_code": "container/shelf/generic/1.0",
                 "json_addl": {
                   "cont_address": {
                     "capacity": "10",
@@ -6858,7 +6858,7 @@
     {
       "name": "Bravo Liquid Handler",
       "polymorphic_discriminator": "equipment_template",
-      "category": "BEQ",
+      "category": "equipment",
       "type": "liquid_handler",
       "subtype": "bravo",
       "version": "1.0",
@@ -6869,10 +6869,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -6904,7 +6904,7 @@
     {
       "name": "Illumnina MiSeq y",
       "polymorphic_discriminator": "equipment_template",
-      "category": "BEQ",
+      "category": "equipment",
       "type": "sequencers",
       "subtype": "miseq-y",
       "version": "1.0",
@@ -6915,10 +6915,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -6950,7 +6950,7 @@
     {
       "name": "Illumnina Novaseq 6000",
       "polymorphic_discriminator": "equipment_template",
-      "category": "BEQ",
+      "category": "equipment",
       "type": "sequencers",
       "subtype": "novaseq-6000",
       "version": "1.0",
@@ -6961,10 +6961,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -6996,7 +6996,7 @@
     {
       "name": "ONT MinION",
       "polymorphic_discriminator": "equipment_template",
-      "category": "BEQ",
+      "category": "equipment",
       "type": "sequencers",
       "subtype": "ont-minion",
       "version": "1.0",
@@ -7007,10 +7007,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -7042,7 +7042,7 @@
     {
       "name": "Generic File",
       "polymorphic_discriminator": "file_template",
-      "category": "BFX",
+      "category": "file",
       "type": "file",
       "subtype": "generic",
       "version": "1.0",
@@ -7053,11 +7053,11 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "download_file": "BAC/file/download_file/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "download_file": "action/file/download_file/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "arbitrary_association_strings": [],
         "cogs": {
@@ -7375,7 +7375,7 @@
     {
       "name": "Generic File Set",
       "polymorphic_discriminator": "file_template",
-      "category": "BFX",
+      "category": "file",
       "type": "file_set",
       "subtype": "generic",
       "version": "1.0",
@@ -7386,10 +7386,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -7469,7 +7469,7 @@
     {
       "name": "Generic Run Set",
       "polymorphic_discriminator": "generic_template",
-      "category": "BGS",
+      "category": "set",
       "type": "run-set",
       "subtype": "generic",
       "version": "1.01",
@@ -7480,8 +7480,8 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "controlled_properties": {},
         "description": "Generic run set for temporary Bloom lab batch and sequencing-run grouping.",
@@ -7570,7 +7570,7 @@
     {
       "name": "Generic File Reference",
       "polymorphic_discriminator": "file_template",
-      "category": "BFX",
+      "category": "file",
       "type": "shared_ref",
       "subtype": "generic",
       "version": "1.0",
@@ -7581,10 +7581,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "arbitrary_association_strings": [],
         "cogs": {
@@ -7656,7 +7656,7 @@
     {
       "name": "Generic Health Event",
       "polymorphic_discriminator": "health_event_template",
-      "category": "BHE",
+      "category": "health",
       "type": "generic",
       "subtype": "health-event",
       "version": "1.0",
@@ -7667,10 +7667,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -7698,7 +7698,7 @@
     {
       "name": "Decision scope for an accession (ACC / TRX / intake bundle).",
       "polymorphic_discriminator": "subject_template",
-      "category": "BSJ",
+      "category": "subject",
       "type": "generic",
       "subtype": "accession-subject",
       "version": "1.0",
@@ -7709,10 +7709,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -7797,7 +7797,7 @@
     {
       "name": "Decision scope for analysis result bundles.",
       "polymorphic_discriminator": "subject_template",
-      "category": "BSJ",
+      "category": "subject",
       "type": "generic",
       "subtype": "analysis-bundle-subject",
       "version": "1.0",
@@ -7808,10 +7808,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -7896,7 +7896,7 @@
     {
       "name": "Fallback decision scope for custom use cases.",
       "polymorphic_discriminator": "subject_template",
-      "category": "BSJ",
+      "category": "subject",
       "type": "generic",
       "subtype": "generic-subject",
       "version": "1.0",
@@ -7907,10 +7907,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -7998,7 +7998,7 @@
     {
       "name": "Decision scope for clinical reportable units.",
       "polymorphic_discriminator": "subject_template",
-      "category": "BSJ",
+      "category": "subject",
       "type": "generic",
       "subtype": "report-subject",
       "version": "1.0",
@@ -8009,10 +8009,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -8097,7 +8097,7 @@
     {
       "name": "Workset grouping workflow steps and objects created during an accessioning transaction.",
       "polymorphic_discriminator": "subject_template",
-      "category": "BSJ",
+      "category": "subject",
       "type": "workset",
       "subtype": "accession",
       "version": "1.0",
@@ -8108,10 +8108,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -8226,7 +8226,7 @@
     {
       "name": "Workset grouping workflow steps and objects created during an extraction batch.",
       "polymorphic_discriminator": "subject_template",
-      "category": "BSJ",
+      "category": "subject",
       "type": "workset",
       "subtype": "extraction",
       "version": "1.0",
@@ -8237,10 +8237,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -8355,7 +8355,7 @@
     {
       "name": "Workset grouping workflow steps and objects created during a sequencing run.",
       "polymorphic_discriminator": "subject_template",
-      "category": "BSJ",
+      "category": "subject",
       "type": "workset",
       "subtype": "sequencing",
       "version": "1.0",
@@ -8366,10 +8366,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -8484,7 +8484,7 @@
     {
       "name": "Workset for carrier-screen 3.9",
       "polymorphic_discriminator": "workflow_template",
-      "category": "BWF",
+      "category": "workflow",
       "type": "assay-workset",
       "subtype": "carrier-screen",
       "version": "3.9",
@@ -8495,11 +8495,11 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "move_among_ay_top_queues": "BAC/move-queues/move-among-ay-top-queues/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "move_among_ay_top_queues": "action/move-queues/move-among-ay-top-queues/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -8519,7 +8519,7 @@
             "relationship_type": "contains",
             "child_templates": [
               {
-                "template_code": "BWS/queue/plasma-isolation-queue-available/1.0",
+                "template_code": "workflow_step/queue/plasma-isolation-queue-available/1.0",
                 "json_addl": {
                   "properties": {
                     "comments": "",
@@ -8528,7 +8528,7 @@
                 }
               },
               {
-                "template_code": "BWS/queue/plasma-isolation-queue-removed/1.0",
+                "template_code": "workflow_step/queue/plasma-isolation-queue-removed/1.0",
                 "json_addl": {
                   "properties": {
                     "comments": "",
@@ -8537,7 +8537,7 @@
                 }
               },
               {
-                "template_code": "BWS/queue/plasma-isolation-queue-exception/1.0",
+                "template_code": "workflow_step/queue/plasma-isolation-queue-exception/1.0",
                 "json_addl": {
                   "properties": {
                     "comments": "",
@@ -8565,7 +8565,7 @@
     {
       "name": "Workset for hla-typing 1.2",
       "polymorphic_discriminator": "workflow_template",
-      "category": "BWF",
+      "category": "workflow",
       "type": "assay-workset",
       "subtype": "hla-typing",
       "version": "1.2",
@@ -8576,11 +8576,11 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "move_among_ay_top_queues": "BAC/move-queues/move-among-ay-top-queues/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "move_among_ay_top_queues": "action/move-queues/move-among-ay-top-queues/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -8618,7 +8618,7 @@
     {
       "name": "Carrier Screen 3.9",
       "polymorphic_discriminator": "workflow_template",
-      "category": "BWF",
+      "category": "workflow",
       "type": "assay",
       "subtype": "carrier-screen",
       "version": "3.9",
@@ -8629,10 +8629,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "assay_type": "assay",
         "cogs": {
@@ -8653,7 +8653,7 @@
             "relationship_type": "contains",
             "child_templates": [
               {
-                "template_code": "BWS/queue/extraction-batch-eligible/1.0",
+                "template_code": "workflow_step/queue/extraction-batch-eligible/1.0",
                 "json_addl": {
                   "description": "Extraction Batch Eligible",
                   "properties": {
@@ -8666,7 +8666,7 @@
                 "name_pattern": "Extraction Batch Eligible"
               },
               {
-                "template_code": "BWS/queue/blood-to-gdna-extraction-eligible/1.0",
+                "template_code": "workflow_step/queue/blood-to-gdna-extraction-eligible/1.0",
                 "json_addl": {
                   "description": "Blood To gDNA Extraction Eligible",
                   "properties": {
@@ -8679,7 +8679,7 @@
                 "name_pattern": "Blood To gDNA Extraction Eligible"
               },
               {
-                "template_code": "BWS/queue/buccal-to-gdna-extraction-eligible/1.0",
+                "template_code": "workflow_step/queue/buccal-to-gdna-extraction-eligible/1.0",
                 "json_addl": {
                   "description": "Buccal To gDNA Extraction Eligible",
                   "properties": {
@@ -8692,7 +8692,7 @@
                 "name_pattern": "Buccal To gDNA Extraction Eligible"
               },
               {
-                "template_code": "BWS/queue/input-gdna-normalization-eligible/1.0",
+                "template_code": "workflow_step/queue/input-gdna-normalization-eligible/1.0",
                 "json_addl": {
                   "description": "Input gDNA Normalization Eligible",
                   "properties": {
@@ -8705,7 +8705,7 @@
                 "name_pattern": "Input gDNA Normalization Eligible"
               },
               {
-                "template_code": "BWS/queue/illumina-novaseq-libprep-eligible/1.0",
+                "template_code": "workflow_step/queue/illumina-novaseq-libprep-eligible/1.0",
                 "json_addl": {
                   "description": "Illumina Novaseq LibPrep Eligible",
                   "properties": {
@@ -8718,7 +8718,7 @@
                 "name_pattern": "Illumina Novaseq LibPrep Eligible"
               },
               {
-                "template_code": "BWS/queue/ont-libprep-eligible/1.0",
+                "template_code": "workflow_step/queue/ont-libprep-eligible/1.0",
                 "json_addl": {
                   "description": "ONT LibPrep Eligible",
                   "properties": {
@@ -8749,7 +8749,7 @@
     {
       "name": "HLA Typing v1.2",
       "polymorphic_discriminator": "workflow_template",
-      "category": "BWF",
+      "category": "workflow",
       "type": "assay",
       "subtype": "hla-typing",
       "version": "1.2",
@@ -8760,10 +8760,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "assay_type": "assay",
         "cogs": {
@@ -8784,7 +8784,7 @@
             "relationship_type": "contains",
             "child_templates": [
               {
-                "template_code": "BWS/queue/extraction-batch-eligible/1.0",
+                "template_code": "workflow_step/queue/extraction-batch-eligible/1.0",
                 "json_addl": {
                   "description": "Extraction Batch Eligible",
                   "properties": {
@@ -8797,7 +8797,7 @@
                 "name_pattern": "Extraction Batch Eligible"
               },
               {
-                "template_code": "BWS/queue/blood-to-gdna-extraction-eligible/1.0",
+                "template_code": "workflow_step/queue/blood-to-gdna-extraction-eligible/1.0",
                 "json_addl": {
                   "description": "Blood To gDNA Extraction Eligible",
                   "properties": {
@@ -8810,7 +8810,7 @@
                 "name_pattern": "Blood To gDNA Extraction Eligible"
               },
               {
-                "template_code": "BWS/queue/buccal-to-gdna-extraction-eligible/1.0",
+                "template_code": "workflow_step/queue/buccal-to-gdna-extraction-eligible/1.0",
                 "json_addl": {
                   "description": "Buccal To gDNA Extraction Eligible",
                   "properties": {
@@ -8823,7 +8823,7 @@
                 "name_pattern": "Buccal To gDNA Extraction Eligible"
               },
               {
-                "template_code": "BWS/queue/input-gdna-normalization-eligible/1.0",
+                "template_code": "workflow_step/queue/input-gdna-normalization-eligible/1.0",
                 "json_addl": {
                   "description": "Input gDNA Normalization Eligible",
                   "properties": {
@@ -8836,7 +8836,7 @@
                 "name_pattern": "Input gDNA Normalization Eligible"
               },
               {
-                "template_code": "BWS/queue/illumina-novaseq-libprep-eligible/1.0",
+                "template_code": "workflow_step/queue/illumina-novaseq-libprep-eligible/1.0",
                 "json_addl": {
                   "description": "Illumina Novaseq LibPrep Eligible",
                   "properties": {
@@ -8849,7 +8849,7 @@
                 "name_pattern": "Illumina Novaseq LibPrep Eligible"
               },
               {
-                "template_code": "BWS/queue/ont-libprep-eligible/1.0",
+                "template_code": "workflow_step/queue/ont-libprep-eligible/1.0",
                 "json_addl": {
                   "description": "ONT LibPrep Eligible",
                   "properties": {
@@ -8880,7 +8880,7 @@
     {
       "name": "Destroy Specimen Containers",
       "polymorphic_discriminator": "workflow_template",
-      "category": "BWF",
+      "category": "workflow",
       "type": "destroy",
       "subtype": "specimen-containers",
       "version": "1.0",
@@ -8891,11 +8891,11 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "destroy_specimen_containers": "BAC/workflow/destroy_specimen_containers/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "destroy_specimen_containers": "action/workflow/destroy_specimen_containers/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -8922,7 +8922,7 @@
     {
       "name": "DNA extraction from blood-whole in tube-strek-10ml tubes to a fixed-plate-96 with gdna in each well.",
       "polymorphic_discriminator": "workflow_template",
-      "category": "BWF",
+      "category": "workflow",
       "type": "extraction",
       "subtype": "blood-whole-to-gdna",
       "version": "1.0",
@@ -8933,10 +8933,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -8968,7 +8968,7 @@
     {
       "name": "DNA extraction from blood-whole in tube-strek-10ml tubes to a fixed-plate-96 with gdna in each well.",
       "polymorphic_discriminator": "workflow_template",
-      "category": "BWF",
+      "category": "workflow",
       "type": "extraction",
       "subtype": "blood-whole-to-plasma-to-cfdna",
       "version": "1.0",
@@ -8979,10 +8979,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9014,7 +9014,7 @@
     {
       "name": "DNA QUANTIFIED",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "analysis",
       "subtype": "gdna-quantified",
       "version": "1.0",
@@ -9025,10 +9025,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9044,44 +9044,44 @@
         "expected_inputs": [
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           }
         ],
         "expected_outputs": [
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           },
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           },
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           },
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           }
         ],
@@ -9107,7 +9107,7 @@
     {
       "name": "Plasma QUANT",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "analysis",
       "subtype": "plasma-quantification",
       "version": "1.0",
@@ -9118,11 +9118,11 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "download_quant_data": "BAC/workflow_step_analysis/download_quant_data/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "download_quant_data": "action/workflow_step_analysis/download_quant_data/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9159,7 +9159,7 @@
     {
       "name": "Specimens Destroyed",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "destroy-steps",
       "subtype": "specimen-containers-destroyed",
       "version": "1.0",
@@ -9170,11 +9170,11 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "complete_specimen_destroy": "BAC/workflow_step_destroy/complete_specimen_destroy/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "complete_specimen_destroy": "action/workflow_step_destroy/complete_specimen_destroy/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9211,7 +9211,7 @@
     {
       "name": "Destroyed Containers Exceptions",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "exception",
       "subtype": "specimen-containers-destroyed",
       "version": "1.0",
@@ -9222,10 +9222,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9262,7 +9262,7 @@
     {
       "name": "cfDNA Extraction Plate ",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "extraction-steps",
       "subtype": "cfdna-extracted",
       "version": "1.0",
@@ -9273,11 +9273,11 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "cfdna_post_extraction_quant": "BAC/workflow_step_extraction/cfdna_post_extraction_quant/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "cfdna_post_extraction_quant": "action/workflow_step_extraction/cfdna_post_extraction_quant/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9294,22 +9294,22 @@
           [
             {
               "container/tube/tube-generic-10ml/*/": {
-                "holds_content": "content/sample/blood-plasma/*"
+                "holds_content": "material/sample/blood-plasma/*"
               }
             },
             {
               "container/tube/tube-generic-10ml/*/": {
-                "holds_content": "content/sample/blood-plasma/*"
+                "holds_content": "material/sample/blood-plasma/*"
               }
             },
             {
               "container/tube/tube-generic-10ml/*/": {
-                "holds_content": "content/sample/blood-plasma/*"
+                "holds_content": "material/sample/blood-plasma/*"
               }
             },
             {
               "container/tube/tube-generic-10ml/*/": {
-                "holds_content": "content/sample/blood-plasma/*"
+                "holds_content": "material/sample/blood-plasma/*"
               }
             }
           ]
@@ -9321,7 +9321,7 @@
                 "child_of_lineages": [
                   {
                     "container/well/fixed-plate-well/*/": {
-                      "holds_content": "content/sample/cfdna/*"
+                      "holds_content": "material/sample/cfdna/*"
                     }
                   }
                 ]
@@ -9332,7 +9332,7 @@
                 "child_of_lineages": [
                   {
                     "container/well/fixed-plate-well/*/": {
-                      "holds_content": "content/sample/cfdna/*"
+                      "holds_content": "material/sample/cfdna/*"
                     }
                   }
                 ]
@@ -9343,7 +9343,7 @@
                 "child_of_lineages": [
                   {
                     "container/well/fixed-plate-well/*/": {
-                      "holds_content": "content/sample/cfdna/*"
+                      "holds_content": "material/sample/cfdna/*"
                     }
                   }
                 ]
@@ -9354,7 +9354,7 @@
                 "child_of_lineages": [
                   {
                     "container/well/fixed-plate-well/*/": {
-                      "holds_content": "content/sample/cfdna/*"
+                      "holds_content": "material/sample/cfdna/*"
                     }
                   }
                 ]
@@ -9384,7 +9384,7 @@
     {
       "name": "Extracting gdna from blood-whole in tubes to wells in a fixed-plate-96.",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "extraction-steps",
       "subtype": "gdna-extraction",
       "version": "1.0",
@@ -9395,10 +9395,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9414,22 +9414,22 @@
         "expected_inputs": [
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           }
         ],
@@ -9440,7 +9440,7 @@
                 "child_of_lineages": [
                   {
                     "container/well/fixed-plate-well/*/": {
-                      "holds_content": "content/sample/gdna/*"
+                      "holds_content": "material/sample/gdna/*"
                     }
                   }
                 ]
@@ -9451,7 +9451,7 @@
                 "child_of_lineages": [
                   {
                     "container/well/fixed-plate-well/*/": {
-                      "holds_content": "content/sample/gdna/*"
+                      "holds_content": "material/sample/gdna/*"
                     }
                   }
                 ]
@@ -9462,7 +9462,7 @@
                 "child_of_lineages": [
                   {
                     "container/well/fixed-plate-well/*/": {
-                      "holds_content": "content/sample/gdna/*"
+                      "holds_content": "material/sample/gdna/*"
                     }
                   }
                 ]
@@ -9473,7 +9473,7 @@
                 "child_of_lineages": [
                   {
                     "container/well/fixed-plate-well/*/": {
-                      "holds_content": "content/sample/gdna/*"
+                      "holds_content": "material/sample/gdna/*"
                     }
                   }
                 ]
@@ -9503,7 +9503,7 @@
     {
       "name": "Loading blood-whole in tube-strek-10ml tubes.",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "extraction-steps",
       "subtype": "loading",
       "version": "1.0",
@@ -9514,10 +9514,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9533,22 +9533,22 @@
         "expected_inputs": [
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           }
         ],
@@ -9575,7 +9575,7 @@
     {
       "name": "plasma isolation",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "extraction-steps",
       "subtype": "plasma-isolated",
       "version": "1.0",
@@ -9586,10 +9586,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9605,44 +9605,44 @@
         "expected_inputs": [
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           },
           {
             "container/tube/tube-strek-10ml/*/": {
-              "holds_content": "content/specimen/blood-whole/*"
+              "holds_content": "material/specimen/blood-whole/*"
             }
           }
         ],
         "expected_outputs": [
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           },
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           },
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           },
           {
             "container/tube/tube-generic-10ml/*/": {
-              "holds_content": "content/sample/blood-plasma/*"
+              "holds_content": "material/sample/blood-plasma/*"
             }
           }
         ],
@@ -9668,7 +9668,7 @@
     {
       "name": "Filled Extraction Plate",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "plate-operations",
       "subtype": "extraction-plate-filled",
       "version": "1.0",
@@ -9679,15 +9679,15 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "cfdna_quant": "BAC/workflow_step_plate_operations/cfdna_quant/1.0",
-          "create_pool_from_containers": "BAC/pool/create_pool_from_containers__extraction_plate_filled/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_child_object": "BAC/object/set-child-object/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0",
-          "stamp_copy_plate": "BAC/workflow_step_plate_operations/stamp_copy_plate/1.0",
-          "stamp_plates_into_plate": "BAC/plate/stamp_plates_into_plate__extraction_plate_filled/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "cfdna_quant": "action/workflow_step_plate_operations/cfdna_quant/1.0",
+          "create_pool_from_containers": "action/pool/create_pool_from_containers__extraction_plate_filled/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_child_object": "action/object/set-child-object/1.0",
+          "set_object_status": "action/core/set_object_status/1.0",
+          "stamp_copy_plate": "action/workflow_step_plate_operations/stamp_copy_plate/1.0",
+          "stamp_plates_into_plate": "action/plate/stamp_plates_into_plate__extraction_plate_filled/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9731,7 +9731,7 @@
     {
       "name": "Heatseal Plate",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "plate-operations",
       "subtype": "heat-seal",
       "version": "1.0",
@@ -9742,10 +9742,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9790,7 +9790,7 @@
     {
       "name": "Existing plate, had 1+ plates merged into it.",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "plate-operations",
       "subtype": "plate-added-to",
       "version": "1.0",
@@ -9801,12 +9801,12 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "cfdna_quant": "BAC/workflow_step_plate_operations/cfdna_quant/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0",
-          "stamp_copy_plate": "BAC/workflow_step_plate_operations/stamp_copy_plate/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "cfdna_quant": "action/workflow_step_plate_operations/cfdna_quant/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0",
+          "stamp_copy_plate": "action/workflow_step_plate_operations/stamp_copy_plate/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9843,7 +9843,7 @@
     {
       "name": "Stamp Copy Plate",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "plate-operations",
       "subtype": "stamp-copy-plate",
       "version": "1.0",
@@ -9854,12 +9854,12 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "cfdna_quant": "BAC/workflow_step_plate_operations/cfdna_quant/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0",
-          "stamp_copy_plate": "BAC/workflow_step_plate_operations/stamp_copy_plate/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "cfdna_quant": "action/workflow_step_plate_operations/cfdna_quant/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0",
+          "stamp_copy_plate": "action/workflow_step_plate_operations/stamp_copy_plate/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9896,7 +9896,7 @@
     {
       "name": "pool",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "pool",
       "subtype": "generic",
       "version": "1.0",
@@ -9907,10 +9907,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9947,7 +9947,7 @@
     {
       "name": "OVERRIDEME",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "queue",
       "subtype": "all-purpose",
       "version": "1.0",
@@ -9958,10 +9958,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -9998,7 +9998,7 @@
     {
       "name": "Blood To gDNA Extraction Eligible",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "queue",
       "subtype": "blood-to-gdna-extraction-eligible",
       "version": "1.0",
@@ -10009,15 +10009,15 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_gdna_to_gdna_normalization_queue": "BAC/workflow_step_queue/add-gdna-to-gdna-normalization-queue/1.0",
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "existing_plate_fill_auto": "BAC/workflow_step_queue/existing-plate-fill-auto/1.0",
-          "existing_plate_fill_directed": "BAC/workflow_step_queue/existing-plate-fill-directed/1.0",
-          "plate_create_fill_auto": "BAC/workflow_step_queue/plate-create-fill-auto/1.0",
-          "plate_create_fill_directed": "BAC/workflow_step_queue/plate-create-fill-directed/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_gdna_to_gdna_normalization_queue": "action/workflow_step_queue/add-gdna-to-gdna-normalization-queue/1.0",
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "existing_plate_fill_auto": "action/workflow_step_queue/existing-plate-fill-auto/1.0",
+          "existing_plate_fill_directed": "action/workflow_step_queue/existing-plate-fill-directed/1.0",
+          "plate_create_fill_auto": "action/workflow_step_queue/plate-create-fill-auto/1.0",
+          "plate_create_fill_directed": "action/workflow_step_queue/plate-create-fill-directed/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -10054,7 +10054,7 @@
     {
       "name": "Buccal To gDNA Extraction Eligible",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "queue",
       "subtype": "buccal-to-gdna-extraction-eligible",
       "version": "1.0",
@@ -10065,15 +10065,15 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_gdna_to_gdna_normalization_queue": "BAC/workflow_step_queue/add-gdna-to-gdna-normalization-queue/1.0",
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "existing_plate_fill_auto": "BAC/workflow_step_queue/existing-plate-fill-auto/1.0",
-          "existing_plate_fill_directed": "BAC/workflow_step_queue/existing-plate-fill-directed/1.0",
-          "plate_create_fill_auto": "BAC/workflow_step_queue/plate-create-fill-auto/1.0",
-          "plate_create_fill_directed": "BAC/workflow_step_queue/plate-create-fill-directed/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_gdna_to_gdna_normalization_queue": "action/workflow_step_queue/add-gdna-to-gdna-normalization-queue/1.0",
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "existing_plate_fill_auto": "action/workflow_step_queue/existing-plate-fill-auto/1.0",
+          "existing_plate_fill_directed": "action/workflow_step_queue/existing-plate-fill-directed/1.0",
+          "plate_create_fill_auto": "action/workflow_step_queue/plate-create-fill-auto/1.0",
+          "plate_create_fill_directed": "action/workflow_step_queue/plate-create-fill-directed/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -10110,7 +10110,7 @@
     {
       "name": "Extraction Batch Eligible",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "queue",
       "subtype": "extraction-batch-eligible",
       "version": "1.0",
@@ -10121,12 +10121,12 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "add_to_blood_gdna_extraction_queue": "BAC/workflow_step_queue/add-to-blood-gdna-extraction-queue/1.0",
-          "add_to_buccal_gdna_extraction_queue": "BAC/workflow_step_queue/add-to-buccal-gdna-extraction-queue/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "add_to_blood_gdna_extraction_queue": "action/workflow_step_queue/add-to-blood-gdna-extraction-queue/1.0",
+          "add_to_buccal_gdna_extraction_queue": "action/workflow_step_queue/add-to-buccal-gdna-extraction-queue/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -10163,7 +10163,7 @@
     {
       "name": "Plasma To Plates For Extraction",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "queue",
       "subtype": "extraction-queue-available",
       "version": "1.0",
@@ -10174,12 +10174,12 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "fill_plate_directed": "BAC/workflow_step_queue/fill_plate_directed/1.0",
-          "fill_plate_undirected": "BAC/workflow_step_queue/fill_plate_undirected/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "fill_plate_directed": "action/workflow_step_queue/fill_plate_directed/1.0",
+          "fill_plate_undirected": "action/workflow_step_queue/fill_plate_undirected/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -10216,7 +10216,7 @@
     {
       "name": "Illumina Novaseq LibPrep Eligible",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "queue",
       "subtype": "illumina-novaseq-libprep-eligible",
       "version": "1.0",
@@ -10227,14 +10227,14 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "existing_plate_fill_auto": "BAC/workflow_step_queue/existing-plate-fill-auto/1.0",
-          "existing_plate_fill_directed": "BAC/workflow_step_queue/existing-plate-fill-directed/1.0",
-          "plate_create_fill_auto": "BAC/workflow_step_queue/plate-create-fill-auto/1.0",
-          "plate_create_fill_directed": "BAC/workflow_step_queue/plate-create-fill-directed/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "existing_plate_fill_auto": "action/workflow_step_queue/existing-plate-fill-auto/1.0",
+          "existing_plate_fill_directed": "action/workflow_step_queue/existing-plate-fill-directed/1.0",
+          "plate_create_fill_auto": "action/workflow_step_queue/plate-create-fill-auto/1.0",
+          "plate_create_fill_directed": "action/workflow_step_queue/plate-create-fill-directed/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -10271,7 +10271,7 @@
     {
       "name": "Input gDNA Normalization Eligible",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "queue",
       "subtype": "input-gdna-normalization-eligible",
       "version": "1.0",
@@ -10282,15 +10282,15 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "existing_plate_fill_auto": "BAC/workflow_step_queue/existing-plate-fill-auto/1.0",
-          "existing_plate_fill_directed": "BAC/workflow_step_queue/existing-plate-fill-directed/1.0",
-          "plate_create_fill_auto": "BAC/workflow_step_queue/plate-create-fill-auto/1.0",
-          "plate_create_fill_directed": "BAC/workflow_step_queue/plate-create-fill-directed/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "save_quant_data": "BAC/workflow_step_queue/save-quant-data/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "existing_plate_fill_auto": "action/workflow_step_queue/existing-plate-fill-auto/1.0",
+          "existing_plate_fill_directed": "action/workflow_step_queue/existing-plate-fill-directed/1.0",
+          "plate_create_fill_auto": "action/workflow_step_queue/plate-create-fill-auto/1.0",
+          "plate_create_fill_directed": "action/workflow_step_queue/plate-create-fill-directed/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "save_quant_data": "action/workflow_step_queue/save-quant-data/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -10327,7 +10327,7 @@
     {
       "name": "ONT LibPrep Eligible",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "queue",
       "subtype": "ont-libprep-eligible",
       "version": "1.0",
@@ -10338,14 +10338,14 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "existing_plate_fill_auto": "BAC/workflow_step_queue/existing-plate-fill-auto/1.0",
-          "existing_plate_fill_directed": "BAC/workflow_step_queue/existing-plate-fill-directed/1.0",
-          "plate_create_fill_auto": "BAC/workflow_step_queue/plate-create-fill-auto/1.0",
-          "plate_create_fill_directed": "BAC/workflow_step_queue/plate-create-fill-directed/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "existing_plate_fill_auto": "action/workflow_step_queue/existing-plate-fill-auto/1.0",
+          "existing_plate_fill_directed": "action/workflow_step_queue/existing-plate-fill-directed/1.0",
+          "plate_create_fill_auto": "action/workflow_step_queue/plate-create-fill-auto/1.0",
+          "plate_create_fill_directed": "action/workflow_step_queue/plate-create-fill-directed/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -10382,7 +10382,7 @@
     {
       "name": "Containers available for plasma isolation in this queue.",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "queue",
       "subtype": "plasma-isolation-queue-available",
       "version": "1.0",
@@ -10393,11 +10393,11 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "link_tubes_auto": "BAC/workflow_step_queue/link_tubes_auto/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "link_tubes_auto": "action/workflow_step_queue/link_tubes_auto/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -10434,7 +10434,7 @@
     {
       "name": "Plasma Isolation Exception Queue",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "queue",
       "subtype": "plasma-isolation-queue-exception",
       "version": "1.0",
@@ -10445,12 +10445,12 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "link_tubes_auto": "BAC/workflow_step_queue/link_tubes_auto/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0",
-          "ycreate_test_req_and_link_child_workflow_step": "BAC/workflow_step_queue/ycreate_test_req_and_link_child_workflow_step/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "link_tubes_auto": "action/workflow_step_queue/link_tubes_auto/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0",
+          "ycreate_test_req_and_link_child_workflow_step": "action/workflow_step_queue/ycreate_test_req_and_link_child_workflow_step/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -10501,7 +10501,7 @@
     {
       "name": "Containers Removed From Queue",
       "polymorphic_discriminator": "workflow_step_template",
-      "category": "BWS",
+      "category": "workflow_step",
       "type": "queue",
       "subtype": "plasma-isolation-queue-removed",
       "version": "1.0",
@@ -10512,10 +10512,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -10563,7 +10563,7 @@
     {
       "name": "Sequencing Library Plate 96",
       "polymorphic_discriminator": "container_template",
-      "category": "BCP",
+      "category": "container",
       "type": "plate",
       "subtype": "sequencing-library-plate-96",
       "version": "1.0",
@@ -10574,12 +10574,12 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "download_plate_map": "BAC/plate/download_plate_map/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0",
-          "stamp_plates_into_plate": "BAC/plate/stamp_plates_into_plate/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "download_plate_map": "action/plate/download_plate_map/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0",
+          "stamp_plates_into_plate": "action/plate/stamp_plates_into_plate/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -12198,7 +12198,7 @@
     {
       "name": "Sequencing Index Plate 96",
       "polymorphic_discriminator": "container_template",
-      "category": "BCP",
+      "category": "container",
       "type": "plate",
       "subtype": "index-plate-96",
       "version": "1.0",
@@ -12209,12 +12209,12 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "download_plate_map": "BAC/plate/download_plate_map/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0",
-          "stamp_plates_into_plate": "BAC/plate/stamp_plates_into_plate/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "download_plate_map": "action/plate/download_plate_map/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0",
+          "stamp_plates_into_plate": "action/plate/stamp_plates_into_plate/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -13833,7 +13833,7 @@
     {
       "name": "Generic Reagent Bottle",
       "polymorphic_discriminator": "container_template",
-      "category": "BCB",
+      "category": "container",
       "type": "bottle",
       "subtype": "generic",
       "version": "1.0",
@@ -13844,10 +13844,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -13881,7 +13881,7 @@
           "container_role": "bottle"
         },
         "valid_content": [
-          "content/.*"
+          "material/.*"
         ],
         "valid_parents": [],
         "semantic_category": "container"
@@ -13890,7 +13890,7 @@
     {
       "name": "Flowcell",
       "polymorphic_discriminator": "container_template",
-      "category": "BCF",
+      "category": "container",
       "type": "flowcell",
       "subtype": "generic",
       "version": "1.0",
@@ -13901,10 +13901,10 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "print_barcode_label": "BAC/core/print_barcode_label/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "print_barcode_label": "action/core/print_barcode_label/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -13937,7 +13937,7 @@
           "lab_code": ""
         },
         "valid_content": [
-          "content/.*"
+          "material/.*"
         ],
         "valid_parents": [],
         "semantic_category": "container"
@@ -13946,7 +13946,7 @@
     {
       "name": "Flowcell Lane",
       "polymorphic_discriminator": "container_template",
-      "category": "BCE",
+      "category": "container",
       "type": "flowcell_lane",
       "subtype": "generic",
       "version": "1.0",
@@ -13957,7 +13957,7 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "cogs": {
           "allocation_type": "",
@@ -13989,7 +13989,7 @@
         },
         "singleton": "0",
         "valid_content": [
-          "content/.*"
+          "material/.*"
         ],
         "valid_parents": [
           "container/plate/fixed-plate.*?/.*?"
@@ -14000,7 +14000,7 @@
     {
       "name": "Saliva Specimen",
       "polymorphic_discriminator": "content_template",
-      "category": "BNA",
+      "category": "material",
       "type": "specimen",
       "subtype": "saliva",
       "version": "1.0",
@@ -14038,7 +14038,7 @@
     {
       "name": "Sequencing Library Content",
       "polymorphic_discriminator": "content_template",
-      "category": "BNQ",
+      "category": "material",
       "type": "sample",
       "subtype": "sequencing-library",
       "version": "1.0",
@@ -14078,7 +14078,7 @@
     {
       "name": "Sequencing Library Pool Content",
       "polymorphic_discriminator": "content_template",
-      "category": "BNP",
+      "category": "material",
       "type": "pool",
       "subtype": "sequencing-library",
       "version": "1.0",
@@ -14117,7 +14117,7 @@
     {
       "name": "Sequencing Index Reagent Content",
       "polymorphic_discriminator": "content_template",
-      "category": "BNX",
+      "category": "material",
       "type": "reagent",
       "subtype": "sequencing-index",
       "version": "1.0",
@@ -14166,7 +14166,7 @@
     {
       "name": "gDNA Quantification Data",
       "polymorphic_discriminator": "data_template",
-      "category": "BDQ",
+      "category": "data",
       "type": "quantification",
       "subtype": "gdna",
       "version": "1.0",
@@ -14177,9 +14177,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Generic data record",
         "expected_inputs": [],
@@ -14207,7 +14207,7 @@
     {
       "name": "Extraction Run Evidence",
       "polymorphic_discriminator": "data_template",
-      "category": "BDX",
+      "category": "data",
       "type": "operation",
       "subtype": "extraction",
       "version": "1.0",
@@ -14218,9 +14218,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Generic data record",
         "expected_inputs": [],
@@ -14245,7 +14245,7 @@
     {
       "name": "Extraction QC Run Evidence",
       "polymorphic_discriminator": "data_template",
-      "category": "BDY",
+      "category": "data",
       "type": "operation",
       "subtype": "extraction-qc",
       "version": "1.0",
@@ -14256,9 +14256,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Generic data record",
         "expected_inputs": [],
@@ -14281,7 +14281,7 @@
     {
       "name": "Library Prep Run Evidence",
       "polymorphic_discriminator": "data_template",
-      "category": "BDP",
+      "category": "data",
       "type": "operation",
       "subtype": "library-prep",
       "version": "1.0",
@@ -14292,9 +14292,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Generic data record",
         "expected_inputs": [],
@@ -14317,7 +14317,7 @@
     {
       "name": "Pooling Run Evidence",
       "polymorphic_discriminator": "data_template",
-      "category": "BDN",
+      "category": "data",
       "type": "operation",
       "subtype": "pooling",
       "version": "1.0",
@@ -14328,9 +14328,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Generic data record",
         "expected_inputs": [],
@@ -14353,7 +14353,7 @@
     {
       "name": "Library Index Assignment Data",
       "polymorphic_discriminator": "data_template",
-      "category": "BDA",
+      "category": "data",
       "type": "library-index-assignment",
       "subtype": "sequencing-library",
       "version": "1.0",
@@ -14364,9 +14364,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Generic data record",
         "expected_inputs": [],
@@ -14391,7 +14391,7 @@
     {
       "name": "Transfer Execution Data",
       "polymorphic_discriminator": "data_template",
-      "category": "BDT",
+      "category": "data",
       "type": "execution",
       "subtype": "transfer",
       "version": "1.0",
@@ -14402,9 +14402,9 @@
       "json_addl": {
         "action_groups": {},
         "action_imports": {
-          "add_relationships": "BAC/core/add-relationships/1.0",
-          "create_subject_and_anchor": "BAC/core/create-subject-and-anchor/1.0",
-          "set_object_status": "BAC/core/set_object_status/1.0"
+          "add_relationships": "action/core/add-relationships/1.0",
+          "create_subject_and_anchor": "action/core/create-subject-and-anchor/1.0",
+          "set_object_status": "action/core/set_object_status/1.0"
         },
         "description": "Generic data record",
         "expected_inputs": [],
@@ -14427,9 +14427,9 @@
     {
       "name": "Bloom Anomaly Record",
       "polymorphic_discriminator": "generic_template",
-      "category": "BAN",
-      "type": "ops",
-      "subtype": "anomaly-record",
+      "category": "ops",
+      "type": "anomaly-record",
+      "subtype": "generic",
       "version": "1.0",
       "instance_prefix": "BAN",
       "instance_polymorphic_identity": "generic_instance",
diff --git a/docs/apis.md b/docs/apis.md
index f283ea6..1f942d3 100644
--- a/docs/apis.md
+++ b/docs/apis.md
@@ -287,7 +287,7 @@ curl -k https://localhost:8912/api/v1/external/specimens \
   -H "Idempotency-Key: atlas-specimen-001" \
   -H "Content-Type: application/json" \
   -d '{
-    "specimen_template_code": "content/specimen/blood-whole/1.0",
+    "specimen_template_code": "material/specimen/blood-whole/1.0",
     "specimen_name": "specimen-demo",
     "status": "active",
     "container_template_code": "container/tube/tube-generic-10ml/1.0",
diff --git a/docs/lab_actions.md b/docs/lab_actions.md
index 3b5ec61..f3d0031 100644
--- a/docs/lab_actions.md
+++ b/docs/lab_actions.md
@@ -19,16 +19,16 @@ The current flow uses the existing Bloom template pack plus one new generic run-
 
 | Purpose | Semantic template path | Instance prefix | Notes |
 |---|---|---:|---|
-| Generic run/set object | `set/run-set/generic/1.01` | `BGS` | New template. Seeded as `category=BGS`, `type=run-set`, `subtype=generic`, `version=1.01`. Holds named sets, run metadata, members, external members, status, and arbitrary metadata. |
+| Generic run/set object | `set/run-set/generic/1.01` | `BGS` | New template. Seeded as `category=set`, `type=run-set`, `subtype=generic`, `version=1.01`. Holds named sets, run metadata, members, external members, status, and arbitrary metadata. |
 | Extraction plate | `container/plate/fixed-plate-96/1.0` | `BCP` | Existing recursive 96-well plate template. Creates linked well containers. |
 | Sequencing-library plate | `container/plate/sequencing-library-plate-96/1.0` | `BCP` | Existing recursive 96-well plate template. Creates linked well containers. |
 | Plate well | `container/well/fixed-plate-well/1.0` | `BCW` | Created by recursive plate templates. |
 | Pool tube | `container/tube/tube-generic-10ml/1.0` | `BCT` | Existing generic tube template. More specific pool-tube templates can be added later if needed. |
-| Incoming specimen contents | `content/specimen/{blood-whole,buccal-swab,saliva}/1.0` | `BNB`, `BNS`, `BNA` | Existing whole-blood, buccal-swab, and saliva specimen templates. Incoming tubes must already hold one content object unless the caller creates/fills the tube first. |
-| Extraction well gDNA | `content/sample/gdna/1.0` | `BNG` | Created during extraction mapping. |
-| Sequencing-library content | `content/sample/sequencing-library/1.0` | `BNQ` | Created during library plate mapping. |
-| Sequencing-library pool content | `content/pool/sequencing-library/1.0` | `BNP` | Created when filling the pool tube. |
-| Sequencing index reagent | `content/reagent/sequencing-index/1.0` | `BNX` | Optional; callers may also store an index barcode string directly. |
+| Incoming specimen contents | `material/specimen/{blood-whole,buccal-swab,saliva}/1.0` | `BNB`, `BNS`, `BNA` | Existing whole-blood, buccal-swab, and saliva specimen templates. Incoming tubes must already hold one material object unless the caller creates/fills the tube first. |
+| Extraction well gDNA | `material/sample/gdna/1.0` | `BNG` | Created during extraction mapping. |
+| Sequencing-library content | `material/sample/sequencing-library/1.0` | `BNQ` | Created during library plate mapping. |
+| Sequencing-library pool content | `material/pool/sequencing-library/1.0` | `BNP` | Created when filling the pool tube. |
+| Sequencing index reagent | `material/reagent/sequencing-index/1.0` | `BNX` | Optional; callers may also store an index barcode string directly. |
 | gDNA quant data | `data/quantification/gdna/1.0` | `BDQ` | Optional per-well extraction output data. |
 
 No additional templates are required for the current implementation. The semantic paths above are the operator-facing shorthand used by the API and docs; the seed file stores Bloom's actual prefix-backed template identity in `category`, `type`, `subtype`, `version`, and `instance_prefix`. If production operators need separate EUID prefixes or stricter metadata for pool tubes, flowcells, reagent sets, or run kits, add those templates as a separate versioned template-pack change and update this matrix before production rollout.
diff --git a/docs/old_docs/ATLAS_BLOOM_CONTRACT_TESTS.md b/docs/old_docs/ATLAS_BLOOM_CONTRACT_TESTS.md
index 790482e..c77dc64 100644
--- a/docs/old_docs/ATLAS_BLOOM_CONTRACT_TESTS.md
+++ b/docs/old_docs/ATLAS_BLOOM_CONTRACT_TESTS.md
@@ -36,7 +36,7 @@ def test_create_container_contract(client):
 ```python
 def test_specimen_crud_contract(client, container_euid):
     create_payload = {
-        "specimen_template_code": "content/specimen/blood-whole/1.0",
+        "specimen_template_code": "material/specimen/blood-whole/1.0",
         "container_euid": container_euid,
         "atlas_refs": {"trf_euid": "TRF-1", "patient_id": "PAT-1", "kit_barcode": "KIT-1"},
         "properties": {"source": "atlas"},
diff --git a/docs/old_docs/TAPDB_SPECIFICATION.md b/docs/old_docs/TAPDB_SPECIFICATION.md
index b796a6d..4901180 100644
--- a/docs/old_docs/TAPDB_SPECIFICATION.md
+++ b/docs/old_docs/TAPDB_SPECIFICATION.md
@@ -998,7 +998,7 @@ Templates are identified by a **template code string** with the format:
 **Examples:**
 - `container/plate/fixed-plate-96/1.0/`
 - `workflow/assay/ngs-library-prep/2.1/`
-- `content/sample/blood-specimen/1.0/`
+- `material/sample/blood-specimen/1.0/`
 - `equipment/instrument/sequencer/1.0/`
 
 ### 4.2 Template JSON Structure
diff --git a/docs/plans/20260520T064952Z_bloom_sequencing_run_ledger.md b/docs/plans/20260520T064952Z_bloom_sequencing_run_ledger.md
index e7be661..9cb8007 100644
--- a/docs/plans/20260520T064952Z_bloom_sequencing_run_ledger.md
+++ b/docs/plans/20260520T064952Z_bloom_sequencing_run_ledger.md
@@ -15,7 +15,7 @@ Add a first-class Bloom sequencing run concept for the Dayhoff-deployed Bloom se
 | Repo state | `git status --short --branch -> ## main...origin/main` |
 | Instructions read | `/Users/jmajor/projects/mega_dayhoff/repos_work/bloom/AGENTS.md`, `/Users/jmajor/projects/mega_dayhoff/dayhoff/AGENTS.md`, `/Users/jmajor/.agents/AGENTS.md`, `/Users/jmajor/.agents/AGENTS.md~`, `/Users/jmajor/.codex/docs/plan-ledger-workflow.md`, `/Users/jmajor/projects/mega_dayhoff/repos_work/bloom/.augment/RULES.md` |
 | Existing pool/run surface | `bloom_lims/api/v1/beta_lab.py` already exposes `POST /api/v1/external/atlas/beta/pools`, `POST /api/v1/external/atlas/beta/runs`, and `GET /api/v1/external/atlas/beta/runs/{run_euid}/resolve` |
-| Existing pool implementation | `bloom_lims/domain/beta_lab_stages.py::create_pool` already creates `content/pool/generic/1.0`, a pool tube, `contains` lineage, and `beta_pool_member` edges |
+| Existing pool implementation | `bloom_lims/domain/beta_lab_stages.py::create_pool` already creates `material/pool/generic/1.0`, a pool tube, `contains` lineage, and `beta_pool_member` edges |
 | Existing run gap | `create_run` stores runs as `data/generic/generic/1.0` with `beta_kind=sequencing_run`; `BetaRunCreateRequest.platform` is `Literal["ILMN"]`; run properties do not have explicit `operator_start_datetime`, `sequencing_end_datetime`, `instrument_euid`, or run subtype |
 | Template gap | `config/tapdb_templates/bloom/templates.json` has `data/wetlab/library_prep_output/1.0` and equipment sequencer templates, but no `data/sequencing_run/*/1.0` templates |
 | Atlas boundary | Bloom `.augment/RULES.md` requires Bloom and Atlas to interact only through published APIs; this change will preserve existing external-reference lineage and not read/write Atlas DBs |
@@ -29,7 +29,7 @@ Add a first-class Bloom sequencing run concept for the Dayhoff-deployed Bloom se
 | BSR-001 | Template pack | Add first-class sequencing run templates with subtypes for Illumina, ONT, and NovaSeq. | SUCCESS | feature_implementation | Gate 3 | orchestrator | `config/tapdb_templates/bloom/templates.json`; live seed verified `BDT/sequencing_run/{illumina,novaseq,ont}/1.0` with EUIDs `Z-TPX-50P`, `Z-TPX-52J`, `Z-TPX-51M` | Missing template-backed sequencing-run data records; runs were generic data rows. | Added and seeded three Bloom-owned sequencing run templates. |
 | BSR-002 | API schema | Extend beta run create/response schema with run subtype, operator start datetime, sequencing end datetime, and instrument linkage while preserving explicit validation. | SUCCESS | feature_implementation | Gate 3 | orchestrator | `bloom_lims/schemas/beta_lab.py`; public `https://bloom.dev.lsmc.life/openapi.json` exposes `platform` enum `ILMN,ONT`, `run_subtype`, `operator_start_datetime`, `sequencing_end_datetime`, and `instrument_euid` | Existing beta run schema only modeled ILMN flowcell runs. | Schema accepts Illumina, ONT, NovaSeq subtype contract and rejects mismatched platform/subtype and naive/out-of-order datetimes. |
 | BSR-003 | Domain persistence | Store sequencing runs using the subtype-specific sequencing run template, link optional instrument via existing `beta_used_instrument`, and preserve pool/library/assignment lineage. | SUCCESS | feature_implementation | Gate 3 | orchestrator | `bloom_lims/domain/beta_lab.py`, `bloom_lims/domain/beta_lab_store.py`, `bloom_lims/domain/beta_lab_stages.py`; local DB-backed `tests/test_queue_flow.py::test_beta_queue_flow_end_to_end` verifies run instance `type=sequencing_run`, `subtype=novaseq`, persisted timing fields, and `beta_used_instrument` lineage | Persistence always created `data/generic/generic/1.0` rows for sequencing runs. | Run creation now chooses `data/sequencing_run/{illumina,ont,novaseq}/1.0` and still keeps pool, library assignment, artifact, and Atlas fulfillment lineage. |
-| BSR-004 | Pool assessment | Verify whether pooled sequencing library already exists and avoid adding a duplicate concept if current `content/pool/generic/1.0` plus pool tube/member lineage satisfies the request. | SUCCESS | feature_implementation | Gate 3 | orchestrator | Existing `create_pool` creates `content/pool/generic/1.0`, pool tube, `contains`, and `beta_pool_member` edges; `tests/test_queue_flow.py::test_beta_queue_flow_end_to_end` exercises that pool before creating the run | Pool concept was uncertain, but not absent. | No duplicate pool model added; existing pool content plus container/member lineage satisfies the request. |
+| BSR-004 | Pool assessment | Verify whether pooled sequencing library already exists and avoid adding a duplicate concept if current `material/pool/generic/1.0` plus pool tube/member lineage satisfies the request. | SUCCESS | feature_implementation | Gate 3 | orchestrator | Existing `create_pool` creates `material/pool/generic/1.0`, pool tube, `contains`, and `beta_pool_member` edges; `tests/test_queue_flow.py::test_beta_queue_flow_end_to_end` exercises that pool before creating the run | Pool concept was uncertain, but not absent. | No duplicate pool model added; existing pool content plus container/member lineage satisfies the request. |
 | BSR-005 | Tests | Add focused tests for sequencing run templates, schema validation, persisted run fields, instrument linkage, and existing pool lineage. | SUCCESS | contract_test | Gate 5 | orchestrator | `pytest tests/test_sequencing_run_contract.py tests/test_queue_flow.py::test_beta_queue_flow_end_to_end tests/test_run_resolver.py::test_run_resolver_returns_404_for_unknown_index -q --no-cov` -> `4 passed`; `jq empty config/tapdb_templates/bloom/templates.json`; `git diff --check` | Contract needed coverage for template loadability and first-class run persistence. | Focused local tests pass. |
 | BSR-006 | Live deploy | Patch AWS-deployed Bloom, seed any new Bloom-owned templates, restart only Bloom, and verify public/auth/readiness behavior. | SUCCESS | contract_test | Gate 5 | orchestrator | Live target `i-09126000eb19643b0`, repo `/home/ubuntu/.cache/dayhoff/local/lsmcok1/repos/bloom`, config `/home/ubuntu/.config/bloom-lsmcok1/bloom-config-lsmcok1.yaml`; `bloom --config ... db seed` -> `seed=ok`; old Bloom PID `238229`, new Bloom PID `264810`; `https://bloom.dev.lsmc.life/readyz` -> `ready=true`, DB `status=ok` | AWS Bloom needed the same template/schema/domain patch and live TapDB seed. | AWS Bloom patched, templates seeded, and only Bloom restarted. |
 
diff --git a/docs/plans/20260618T000000Z_bloom_lab_action_flow_ledger.md b/docs/plans/20260618T000000Z_bloom_lab_action_flow_ledger.md
index a2befa9..b9d5ade 100644
--- a/docs/plans/20260618T000000Z_bloom_lab_action_flow_ledger.md
+++ b/docs/plans/20260618T000000Z_bloom_lab_action_flow_ledger.md
@@ -15,7 +15,7 @@ Build a Bloom-owned lab actions layer for extraction plates, sequencing library
 - Existing primitives found:
   - recursive template create in `BloomObj.create_instances`
   - `container/plate/fixed-plate-96/1.0`, `container/plate/sequencing-library-plate-96/1.0`, `container/well/fixed-plate-well/1.0`
-  - `content/sample/gdna/1.0`, `content/sample/sequencing-library/1.0`, `content/pool/sequencing-library/1.0`, `content/reagent/sequencing-index/1.0`
+  - `material/sample/gdna/1.0`, `material/sample/sequencing-library/1.0`, `material/pool/sequencing-library/1.0`, `material/reagent/sequencing-index/1.0`
   - `data/quantification/gdna/1.0`, `data/sequencing_run/*/1.0`
   - Zebra Day service wrapper for print dispatch
 
@@ -57,19 +57,19 @@ Build a Bloom-owned lab actions layer for extraction plates, sequencing library
 - `source ./activate dev && python -m pytest tests/test_lab_actions_api.py tests/test_bloom_prefix_taxonomy.py::test_wet_lab_templates_use_bloom_prefix_taxonomy tests/test_route_coverage_gaps_api.py::test_object_creation_plate_creates_96_linked_wells tests/test_template_instantiation_recursion.py tests/test_api_v1.py::TestObjectCreationAPI tests/test_api_v1.py::TestObjectCreationPathTraversal -q --cov-reset --cov=bloom_lims.api.v1.lab_actions --cov=bloom_lims.domain.lab_actions --cov=bloom_lims.schemas.lab_actions --cov=bloom_lims.api.v1.object_creation --cov=bloom_lims.schemas.objects --cov-report=term-missing --cov-report=json:coverage-lab-actions.json --cov-fail-under=81` -> 30 passed; total changed-surface coverage 83.81%.
 - Full repo test collection is not clean in the local Bloom env: `tests/test_beta_cross_repo_smoke.py` imports Ursa and requires `daylily-ephemeral-cluster`; broad non-E2E collection also stalled before progress in local subprocess handling. These are not lab-action source failures.
 - Template inventory from `config/tapdb_templates/bloom/templates.json` confirmed these seeded records for the lab-action flow:
-  - `BGS/run-set/generic/1.01`
-  - `BCP/plate/fixed-plate-96/1.0`
-  - `BCP/plate/sequencing-library-plate-96/1.0`
-  - `BCW/well/fixed-plate-well/1.0`
-  - `BCT/tube/tube-generic-10ml/1.0`
-  - `BNB/specimen/blood-whole/1.0`
-  - `BNS/specimen/buccal-swab/1.0`
-  - `BNA/specimen/saliva/1.0`
-  - `BNG/sample/gdna/1.0`
-  - `BNQ/sample/sequencing-library/1.0`
-  - `BNP/pool/sequencing-library/1.0`
-  - `BNX/reagent/sequencing-index/1.0`
-  - `BDQ/quantification/gdna/1.0`
+  - `set/run-set/generic/1.01`
+  - `container/plate/fixed-plate-96/1.0`
+  - `container/plate/sequencing-library-plate-96/1.0`
+  - `container/well/fixed-plate-well/1.0`
+  - `container/tube/tube-generic-10ml/1.0`
+  - `material/specimen/blood-whole/1.0`
+  - `material/specimen/buccal-swab/1.0`
+  - `material/specimen/saliva/1.0`
+  - `material/sample/gdna/1.0`
+  - `material/sample/sequencing-library/1.0`
+  - `material/pool/sequencing-library/1.0`
+  - `material/reagent/sequencing-index/1.0`
+  - `data/quantification/gdna/1.0`
 - Local browser proof used repo test-runtime config plus `BLOOM_OAUTH=no`; Playwright captured `/lab-actions` at `output/playwright/bloom_lab_actions/lab_actions_wizard_local.png`.
 - Local browser console still shows the pre-existing `/api/v1/me/preferences` 503 under test-runtime config; `/lab-actions` itself returned 200 and static assets loaded.
 - Docs pass added `docs/lab_actions.md` and linked it from `README.md`, `docs/apis.md`, `docs/gui.md`, and `docs/architecture.md`.
diff --git a/pyproject.toml b/pyproject.toml
index 0c96472..f6171e5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,7 +28,7 @@ license = {text = "MIT"}
 requires-python = ">=3.12"
 dependencies = [
     "cli-core-yo==2.1.1",
-    "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.5",
+    "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.6",
     "daylily-auth-cognito==2.1.5",
     "IPython>=8.18.1",
     "bandit[toml]>=1.8.0",
diff --git a/tests/test_atlas_workflow_contract.py b/tests/test_atlas_workflow_contract.py
index 3d2eb6d..070cf54 100644
--- a/tests/test_atlas_workflow_contract.py
+++ b/tests/test_atlas_workflow_contract.py
@@ -142,7 +142,7 @@ def _create_specimen_payload(
     container_euid: str | None = None,
 ) -> dict:
     payload = {
-        "specimen_template_code": "content/specimen/blood-whole/1.0",
+        "specimen_template_code": "material/specimen/blood-whole/1.0",
         "specimen_name": f"specimen-{_suffix()}",
         "status": "active",
         "properties": {"source": "atlas-contract-test"},
@@ -260,7 +260,7 @@ def get_container_trf_context(
             "/api/v1/external/specimens",
             headers={"Idempotency-Key": _opaque("idem", 16)},
             json={
-                "specimen_template_code": "content/specimen/blood-whole/1.0",
+                "specimen_template_code": "material/specimen/blood-whole/1.0",
                 "specimen_name": "context-mismatch",
                 "container_euid": container["euid"],
                 "status": "active",
@@ -315,7 +315,7 @@ def get_container_trf_context(
         created = _create_specimen(
             client,
             payload={
-                "specimen_template_code": "content/specimen/blood-whole/1.0",
+                "specimen_template_code": "material/specimen/blood-whole/1.0",
                 "specimen_name": "context-match",
                 "container_euid": container["euid"],
                 "status": "active",
@@ -408,7 +408,7 @@ def test_unsupported_template_returns_validation_error(monkeypatch):
         response = client.post(
             "/api/v1/external/specimens",
             json={
-                "specimen_template_code": "content/specimen/saliva/1.0",
+                "specimen_template_code": "material/specimen/saliva/1.0",
                 "specimen_name": "unsupported-template",
                 "status": "active",
                 "atlas_refs": {"patient_id": f"PAT-{_suffix()}"},
diff --git a/tests/test_bloom_prefix_taxonomy.py b/tests/test_bloom_prefix_taxonomy.py
index 12b3181..901f31d 100644
--- a/tests/test_bloom_prefix_taxonomy.py
+++ b/tests/test_bloom_prefix_taxonomy.py
@@ -24,9 +24,8 @@ def _template_pack() -> dict:
 def _templates_by_code() -> dict[str, dict]:
     templates: dict[str, dict] = {}
     for template in _template_pack()["templates"]:
-        semantic_category = template["json_addl"].get("semantic_category")
         code = (
-            f"{semantic_category}/{template['type']}/"
+            f"{template['category']}/{template['type']}/"
             f"{template['subtype']}/{template['version']}"
         )
         templates[code] = template
@@ -45,14 +44,14 @@ def test_wet_lab_templates_use_bloom_prefix_taxonomy() -> None:
         "container/bottle/generic/1.0": "BCB",
         "container/flowcell/generic/1.0": "BCF",
         "container/flowcell_lane/generic/1.0": "BCE",
-        "content/specimen/blood-whole/1.0": "BNB",
-        "content/specimen/buccal-swab/1.0": "BNS",
-        "content/specimen/saliva/1.0": "BNA",
-        "content/sample/gdna/1.0": "BNG",
-        "content/sample/cfdna/1.0": "BNC",
-        "content/sample/sequencing-library/1.0": "BNQ",
-        "content/pool/sequencing-library/1.0": "BNP",
-        "content/reagent/sequencing-index/1.0": "BNX",
+        "material/specimen/blood-whole/1.0": "BNB",
+        "material/specimen/buccal-swab/1.0": "BNS",
+        "material/specimen/saliva/1.0": "BNA",
+        "material/sample/gdna/1.0": "BNG",
+        "material/sample/cfdna/1.0": "BNC",
+        "material/sample/sequencing-library/1.0": "BNQ",
+        "material/pool/sequencing-library/1.0": "BNP",
+        "material/reagent/sequencing-index/1.0": "BNX",
         "data/generic/gdna-quantification/1.0": "BDQ",
         "data/quantification/gdna/1.0": "BDQ",
         "data/operation/extraction/1.0": "BDX",
@@ -67,7 +66,7 @@ def test_wet_lab_templates_use_bloom_prefix_taxonomy() -> None:
 
     for code, expected_prefix in expected_prefixes.items():
         template = templates[code]
-        assert template["category"] == expected_prefix
+        assert template["category"] != expected_prefix
         assert template["instance_prefix"] == expected_prefix
 
 
@@ -82,7 +81,7 @@ def test_anomaly_template_is_packaged_for_observability() -> None:
             template["subtype"],
             template["version"],
         )
-        == ("BAN", "ops", "anomaly-record", "1.0")
+        == ("ops", "anomaly-record", "generic", "1.0")
     )
 
     assert anomaly["instance_prefix"] == "BAN"
@@ -171,12 +170,10 @@ def test_readme_documents_taxonomy_and_historical_object_rule() -> None:
     readme = (PROJECT_ROOT / "README.md").read_text(encoding="utf-8")
 
     for snippet in (
-        "BC*` | Containers",
-        "BN*` | Contents, materials, and reagents",
-        "BD*` | Data and evidence objects",
-        "BR*` | Runs and executions",
-        "BG*` | Generic helpers and external-object mappings",
+        "Bloom models physical/material execution",
+        "containers, materials/content, equipment",
+        "recursive template creation",
         "Existing historical objects keep their already minted EUIDs",
-        "Prefixes are governance and display labels only",
+        "issuance and governance labels only",
     ):
         assert snippet in readme
diff --git a/tests/test_cli_db_command_paths.py b/tests/test_cli_db_command_paths.py
index ff04b28..d9aba92 100644
--- a/tests/test_cli_db_command_paths.py
+++ b/tests/test_cli_db_command_paths.py
@@ -489,23 +489,23 @@ def test_seed_templates_split_core_and_client_ownership(
         lambda _dirs, strict: (
             [
                 {
-                    "category": "SYS",
-                    "type": "system",
-                    "subtype": "config",
+                    "category": "actor",
+                    "type": "user",
+                    "subtype": "system",
                     "version": "1.0",
                     "instance_prefix": "SYS",
                     "_source_file": str(core_template_path),
                 },
                 {
-                    "category": "XRF",
-                    "type": "reference",
-                    "subtype": "external_object",
+                    "category": "reference",
+                    "type": "external_identifier",
+                    "subtype": "tapdb_object",
                     "version": "1.0",
                     "instance_prefix": "XRF",
                     "_source_file": str(core_template_path),
                 },
                 {
-                    "category": "BAC",
+                    "category": "action",
                     "type": "beta_lab",
                     "subtype": "claim_material_in_queue",
                     "version": "1.0",
@@ -615,31 +615,34 @@ def dispose(self):
 def test_retire_obsolete_template_variants_only_deletes_stale_prefixes() -> None:
     templates = [
         {
-            "category": "BRM",
+            "category": "data",
             "type": "sequencing_run",
             "subtype": "illumina",
             "version": "1.0",
+            "instance_prefix": "BRM",
             "json_addl": {"semantic_category": "data"},
         },
         {
-            "category": "BRN",
+            "category": "data",
             "type": "sequencing_run",
             "subtype": "ont",
             "version": "1.0",
+            "instance_prefix": "BRN",
             "json_addl": {"semantic_category": "data"},
         },
         {
-            "category": "BCT",
+            "category": "container",
             "type": "tube",
             "subtype": "tube-generic-10ml",
             "version": "1.0",
+            "instance_prefix": "BCN",
             "json_addl": {"semantic_category": "container"},
         },
     ]
     current = SimpleNamespace(
         domain_code="Z",
         type="sequencing_run",
-        category="BRM",
+        category="data",
         subtype="illumina",
         version="1.0",
         is_deleted=False,
@@ -728,14 +731,16 @@ def flush(self):
         domain_code="Z",
     )
 
-    assert retired == 2
+    assert retired == 4
     assert current.is_deleted is False
     assert stale_prefix.is_deleted is True
     assert stale_prefix.bstatus == "retired"
-    assert stale_subtype.is_deleted is False
+    assert stale_subtype.is_deleted is True
+    assert stale_subtype.bstatus == "retired"
     assert stale_container_prefix.is_deleted is True
     assert stale_container_prefix.bstatus == "retired"
-    assert non_data.is_deleted is False
+    assert non_data.is_deleted is True
+    assert non_data.bstatus == "retired"
     assert fake_session.flushed == 1
 
 
diff --git a/tests/test_core_validation.py b/tests/test_core_validation.py
index 0301f3d..388e728 100644
--- a/tests/test_core_validation.py
+++ b/tests/test_core_validation.py
@@ -224,7 +224,7 @@ def test_valid_reference_pattern(self):
         # Valid patterns
         assert validator._is_valid_reference("action/generic/test/1.0")
         assert validator._is_valid_reference("workflow/dna_extraction/v1/1.0")
-        assert validator._is_valid_reference("content/sample/blood/*/")
+        assert validator._is_valid_reference("material/sample/blood/*/")
 
         # Invalid patterns
         assert not validator._is_valid_reference("invalid")
diff --git a/tests/test_packaging_metadata.py b/tests/test_packaging_metadata.py
index 0aa2123..63c5e79 100644
--- a/tests/test_packaging_metadata.py
+++ b/tests/test_packaging_metadata.py
@@ -15,7 +15,7 @@ def test_project_dependencies_pin_release_train_versions() -> None:
 
     assert "cli-core-yo==2.1.1" in dependencies
     assert "daylily-auth-cognito==2.1.5" in dependencies
-    assert "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.4" in dependencies
+    assert "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.6" in dependencies
     assert "IPython>=8.18.1" in dependencies
     assert "psycopg2-binary==2.9.12" in dependencies
     assert not any(str(dep).startswith("zebra-day") for dep in dependencies)
diff --git a/tests/test_sequencing_run_contract.py b/tests/test_sequencing_run_contract.py
index cb6d1c2..d689d84 100644
--- a/tests/test_sequencing_run_contract.py
+++ b/tests/test_sequencing_run_contract.py
@@ -63,7 +63,7 @@ def test_sequencing_run_templates_are_shipped_for_tapdb_seed():
     for template_key, (platform, instance_prefix) in expected.items():
         template = templates[template_key]
         props = template["json_addl"]["properties"]
-        assert template["category"] == instance_prefix
+        assert template["category"] == "data"
         assert template["instance_prefix"] == instance_prefix
         assert template["json_addl"]["semantic_category"] == "data"
         assert props["beta_kind"] == "sequencing_run"
diff --git a/uv.lock b/uv.lock
index 335c05a..74ffb0e 100644
--- a/uv.lock
+++ b/uv.lock
@@ -200,7 +200,7 @@ requires-dist = [
     { name = "cli-core-yo", specifier = "==2.1.1" },
     { name = "daylily-auth-cognito", specifier = "==2.1.5" },
     { name = "daylily-carrier-tracking", specifier = "==0.5.1" },
-    { name = "daylily-tapdb", git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.5" },
+    { name = "daylily-tapdb", git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.6" },
     { name = "djlint" },
     { name = "fastapi", specifier = ">=0.110.0" },
     { name = "httpx", specifier = ">=0.27.2" },
@@ -704,8 +704,8 @@ wheels = [
 
 [[package]]
 name = "daylily-tapdb"
-version = "9.0.5"
-source = { git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.5#0230d3c9bc8e3ef49e948ce3f8a7169b8e90a0be" }
+version = "9.0.6"
+source = { git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.6#ea195137638d1cc49b4499c9bf778c57b6d70d9b" }
 dependencies = [
     { name = "cli-core-yo" },
     { name = "jsonschema" },

From af6b81bbf69e8096f538018e5771220451a01abb Mon Sep 17 00:00:00 2001
From: John Major 
Date: Fri, 19 Jun 2026 09:50:38 -0700
Subject: [PATCH 44/47] Add Bloom container action API and GUI

---
 bloom_lims/api/v1/__init__.py           |   3 +
 bloom_lims/api/v1/container_actions.py  | 248 ++++++++++++++++++++++++
 bloom_lims/gui/routes/modern.py         |  13 ++
 templates/modern/base.html              |   3 +
 templates/modern/container_actions.html | 155 +++++++++++++++
 tests/test_lab_actions_api.py           | 108 +++++++++++
 6 files changed, 530 insertions(+)
 create mode 100644 bloom_lims/api/v1/container_actions.py
 create mode 100644 templates/modern/container_actions.html

diff --git a/bloom_lims/api/v1/__init__.py b/bloom_lims/api/v1/__init__.py
index 0c03ab7..7fd8888 100644
--- a/bloom_lims/api/v1/__init__.py
+++ b/bloom_lims/api/v1/__init__.py
@@ -21,6 +21,7 @@
 from .batch import router as batch_router
 from .beta_lab import router as beta_lab_router
 from .containers import router as containers_router
+from .container_actions import router as container_actions_router
 from .content import router as content_router
 from .equipment import router as equipment_router
 from .execution_queue import router as execution_queue_router
@@ -45,6 +46,7 @@
 router.include_router(auth_router)
 router.include_router(preferences_router)
 router.include_router(containers_router)
+router.include_router(container_actions_router)
 router.include_router(content_router)
 router.include_router(equipment_router)
 router.include_router(execution_queue_router)
@@ -77,6 +79,7 @@ async def api_v1_info():
             "objects": "/api/v1/objects",
             "auth": "/api/v1/auth",
             "containers": "/api/v1/containers",
+            "container_actions": "/api/v1/container-actions",
             "content": "/api/v1/content",
             "equipment": "/api/v1/equipment",
             "execution": "/api/v1/execution",
diff --git a/bloom_lims/api/v1/container_actions.py b/bloom_lims/api/v1/container_actions.py
new file mode 100644
index 0000000..440324f
--- /dev/null
+++ b/bloom_lims/api/v1/container_actions.py
@@ -0,0 +1,248 @@
+"""Generic Bloom container-action validation facade."""
+
+from __future__ import annotations
+
+import csv
+from io import StringIO
+from typing import Any, Literal
+
+from fastapi import APIRouter, Depends, HTTPException
+from pydantic import BaseModel, Field, ValidationError
+from sqlalchemy import select
+
+from bloom_lims.tapdb_adapter import BLOOMdb3, generic_instance
+from bloom_lims.domain.lab_actions import LabActionsService
+from bloom_lims.schemas.lab_actions import (
+    ExtractionPlateRequest,
+    ExtractionQcPlateRequest,
+    LabSetRequest,
+    PlateWellDataRequest,
+    PrintEuidRequest,
+    SeqLibraryPlateRequest,
+    SeqLibraryPoolRequest,
+    SeqRunSetRequest,
+)
+
+from .dependencies import APIUser, require_write
+
+router = APIRouter(prefix="/container-actions", tags=["Container Actions"])
+
+
+class ContainerActionScanRequest(BaseModel):
+    rows: str | None = None
+    records: list[dict[str, Any]] = Field(default_factory=list)
+    default_target: str | None = None
+    child_name: str | None = None
+    child_description: str | None = None
+    child_content_type: str | None = None
+
+
+ContainerActionOperation = Literal[
+    "extraction_plate",
+    "extraction_qc_plate",
+    "plate_well_data",
+    "seq_library_plate",
+    "seq_library_pool",
+    "seq_run_set",
+    "lab_set",
+    "print_euids",
+]
+
+
+class ContainerActionExecuteRequest(ContainerActionScanRequest):
+    operation_type: ContainerActionOperation | None = None
+    operation_payload: dict[str, Any] | None = None
+
+
+def _service_for_user(user: APIUser) -> LabActionsService:
+    return LabActionsService(
+        BLOOMdb3(app_username=user.email),
+        user_id=user.user_id,
+        email=user.email,
+    )
+
+
+def _split_source(value: str) -> tuple[str, str | None]:
+    source = str(value or "").strip()
+    if not source:
+        raise ValueError("source EUID is required")
+    if "." not in source:
+        return source, None
+    euid, well = source.rsplit(".", 1)
+    euid = euid.strip()
+    well = well.strip().upper()
+    if not euid or not well:
+        raise ValueError(f"Invalid source well reference: {value!r}")
+    return euid, well
+
+
+def _normalize_record(row: dict[str, Any], default_target: str | None) -> dict[str, Any]:
+    source = row.get("source") or row.get("source_euid") or row.get("euid") or row.get("0")
+    target = (
+        row.get("target")
+        or row.get("target_container_euid")
+        or row.get("target_container")
+        or row.get("1")
+        or default_target
+    )
+    target_well = row.get("target_well") or row.get("well") or row.get("2")
+    source_euid, source_well = _split_source(str(source or ""))
+    target_text = str(target or "").strip()
+    if not target_text:
+        raise ValueError(f"Target is required for source {source_euid}")
+    create_type = None
+    target_euid = target_text
+    if target_text.upper().startswith("CREATE."):
+        create_type = target_text.split(".", 1)[1].strip()
+        target_euid = None
+        if not create_type:
+            raise ValueError(f"CREATE target requires a type for source {source_euid}")
+    return {
+        "source_euid": source_euid,
+        "source_well": source_well,
+        "target_euid": target_euid,
+        "create_type": create_type,
+        "target_well": str(target_well or "").strip().upper() or None,
+        "mapping_mode": "directed" if target_well else "auto",
+    }
+
+
+def _parse_rows(payload: ContainerActionScanRequest) -> list[dict[str, Any]]:
+    records = list(payload.records)
+    if payload.rows:
+        sample = payload.rows[:1024]
+        try:
+            dialect = csv.Sniffer().sniff(sample, delimiters=",\t")
+        except csv.Error:
+            dialect = csv.excel
+        reader = csv.reader(StringIO(payload.rows), dialect)
+        for row in reader:
+            if not row or not any(str(cell).strip() for cell in row):
+                continue
+            records.append({str(index): value for index, value in enumerate(row)})
+    if not records:
+        raise ValueError("rows or records is required")
+    return [_normalize_record(row, payload.default_target) for row in records]
+
+
+def _object_kind(euid: str, user: APIUser) -> dict[str, Any]:
+    db = BLOOMdb3(app_username=user.email)
+    try:
+        instance = db.session.execute(
+            select(generic_instance).where(
+                generic_instance.euid == euid,
+                generic_instance.is_deleted.is_(False),
+            )
+        ).scalar_one_or_none()
+        if instance is None:
+            return {"euid": euid, "exists": False, "kind": None}
+        return {
+            "euid": euid,
+            "exists": True,
+            "kind": "/".join(
+                [
+                    str(getattr(instance, "category", "") or ""),
+                    str(getattr(instance, "type", "") or ""),
+                    str(getattr(instance, "subtype", "") or ""),
+                    str(getattr(instance, "version", "") or ""),
+                ]
+            ),
+        }
+    finally:
+        db.close()
+
+
+@router.post("/validate")
+async def validate_container_action(
+    payload: ContainerActionScanRequest,
+    user: APIUser = Depends(require_write),
+):
+    try:
+        planned = _parse_rows(payload)
+        source_types = {row["source_euid"]: _object_kind(row["source_euid"], user) for row in planned}
+        target_types = {
+            row["target_euid"]: _object_kind(row["target_euid"], user)
+            for row in planned
+            if row["target_euid"]
+        }
+        return {
+            "valid": True,
+            "row_count": len(planned),
+            "planned": planned,
+            "source_types": source_types,
+            "target_types": target_types,
+            "creates": [row for row in planned if row["create_type"]],
+        }
+    except (ValueError, ValidationError) as exc:
+        raise HTTPException(status_code=400, detail=str(exc)) from exc
+
+
+@router.post("/execute")
+async def execute_container_action(
+    payload: ContainerActionExecuteRequest,
+    user: APIUser = Depends(require_write),
+):
+    validation = await validate_container_action(payload, user)
+    if not payload.operation_type:
+        raise HTTPException(
+            status_code=400,
+            detail={
+                "message": (
+                    "operation_type is required. Container actions do not infer "
+                    "execution behavior from scanned rows."
+                ),
+                "validation": validation,
+            },
+        )
+    if not payload.operation_payload:
+        raise HTTPException(
+            status_code=400,
+            detail={
+                "message": "operation_payload is required for container-action execution.",
+                "operation_type": payload.operation_type,
+                "validation": validation,
+            },
+        )
+
+    service = _service_for_user(user)
+    try:
+        operation_payload = payload.operation_payload
+        if payload.operation_type == "extraction_plate":
+            result = service.create_extraction_plate(
+                ExtractionPlateRequest.model_validate(operation_payload)
+            )
+        elif payload.operation_type == "extraction_qc_plate":
+            result = service.fill_extraction_qc_plate(
+                ExtractionQcPlateRequest.model_validate(operation_payload)
+            )
+        elif payload.operation_type == "plate_well_data":
+            result = service.attach_plate_well_data(
+                PlateWellDataRequest.model_validate(operation_payload)
+            )
+        elif payload.operation_type == "seq_library_plate":
+            result = service.create_seq_library_plate(
+                SeqLibraryPlateRequest.model_validate(operation_payload)
+            )
+        elif payload.operation_type == "seq_library_pool":
+            result = service.create_seq_library_pool(
+                SeqLibraryPoolRequest.model_validate(operation_payload)
+            )
+        elif payload.operation_type == "seq_run_set":
+            result = service.create_seq_run_set(
+                SeqRunSetRequest.model_validate(operation_payload)
+            )
+        elif payload.operation_type == "lab_set":
+            result = service.create_lab_set(LabSetRequest.model_validate(operation_payload))
+        elif payload.operation_type == "print_euids":
+            result = service.print_euids(PrintEuidRequest.model_validate(operation_payload))
+        else:  # pragma: no cover - Literal validation should prevent this.
+            raise HTTPException(status_code=400, detail="Unsupported operation_type")
+        return {
+            "operation_type": payload.operation_type,
+            "validation": validation,
+            "result": result,
+        }
+    except ValueError as exc:
+        raise HTTPException(status_code=400, detail=str(exc)) from exc
+    finally:
+        service.close()
diff --git a/bloom_lims/gui/routes/modern.py b/bloom_lims/gui/routes/modern.py
index abff4b4..27a57c3 100644
--- a/bloom_lims/gui/routes/modern.py
+++ b/bloom_lims/gui/routes/modern.py
@@ -175,6 +175,19 @@ async def lab_actions_wizard(request: Request, _auth=Depends(require_auth)):
     return HTMLResponse(content=template.render(context), status_code=200)
 
 
+@router.get("/container-actions", response_class=HTMLResponse)
+async def container_actions_wizard(request: Request, _auth=Depends(require_auth)):
+    user_data = request.session.get("user_data", {})
+    template = templates.get_template("modern/container_actions.html")
+    context = {
+        "request": request,
+        "udat": user_data,
+        "user": user_data,
+        "page_title": "Container Actions",
+    }
+    return HTMLResponse(content=template.render(context), status_code=200)
+
+
 @router.get("/help", response_class=HTMLResponse)
 async def help_page(request: Request):
     user_data = request.session.get("user_data", {})
diff --git a/templates/modern/base.html b/templates/modern/base.html
index d694f78..1afaa87 100644
--- a/templates/modern/base.html
+++ b/templates/modern/base.html
@@ -72,6 +72,9 @@
             
                  Lab Actions
             
+            
+                 Container Actions
+            
             

                 
                      Tools 
diff --git a/templates/modern/container_actions.html b/templates/modern/container_actions.html
new file mode 100644
index 0000000..a7c5600
--- /dev/null
+++ b/templates/modern/container_actions.html
@@ -0,0 +1,155 @@
+{% extends "modern/base.html" %}
+
+{% block title %}Container Actions - BLOOM{% endblock %}
+
+{% block content %}
+

+    

+        
Container Actions

+        
Validate scanned container mappings, then execute an explicit lab action API payload.

+    

+

+
+

+    

+        

+            
Scan or Upload Rows

+        

+        

+            
+            
+
+            

+                

+                    
+                    
+                

+                

+                    
+                    
+                

+            

+
+            

+                
+            

+        

+    

+
+    

+        

+            
Execute Explicit Operation

+        

+        

+            
+            
+
+            
+            
+
+            

+                
+            

+        

+    

+

+
+

+    

+        
Validation And Execution Result

+    

+    

+        
Ready.

+        
{}

+    

+

+{% endblock %}
+
+{% block extra_js %}
+
+{% endblock %}
diff --git a/tests/test_lab_actions_api.py b/tests/test_lab_actions_api.py
index 011a05b..616b867 100644
--- a/tests/test_lab_actions_api.py
+++ b/tests/test_lab_actions_api.py
@@ -12,6 +12,7 @@
 
 from fastapi.testclient import TestClient
 
+from bloom_lims.api.v1 import container_actions as container_actions_api
 from bloom_lims.domain.lab_action_spreadsheets import parse_workbook
 from main import app
 
@@ -216,6 +217,99 @@ def test_lab_actions_full_ilmn_flow_and_csv_export() -> None:
         assert library_content in sample_sheet.text
 
 
+def test_container_actions_validate_and_explicit_execute_dispatch(monkeypatch) -> None:
+    client = _client()
+    tube_euid = "Z-BCT-CONTAINER-ACTION"
+
+    def fake_object_kind(euid, user):
+        return {
+            "euid": euid,
+            "exists": True,
+            "kind": "container/tube/tube-generic-10ml/1.0",
+        }
+
+    monkeypatch.setattr(container_actions_api, "_object_kind", fake_object_kind)
+
+    validation = client.post(
+        "/api/v1/container-actions/validate",
+        json={
+            "rows": f"{tube_euid},CREATE.container/plate/96-well/1.0,A1\n",
+            "child_name": "pytest container action plate",
+            "child_content_type": "content/gdna/generic/1.0",
+        },
+    )
+    assert validation.status_code == 200, validation.text
+    payload = validation.json()
+    assert payload["valid"] is True
+    assert payload["row_count"] == 1
+    assert payload["planned"][0]["source_euid"] == tube_euid
+    assert payload["planned"][0]["create_type"] == "container/plate/96-well/1.0"
+    assert payload["planned"][0]["target_well"] == "A1"
+    assert payload["source_types"][tube_euid]["exists"] is True
+
+    tsv_validation = client.post(
+        "/api/v1/container-actions/validate",
+        json={
+            "rows": f"{tube_euid}\tCREATE.container/plate/96-well/1.0\tB2\n",
+            "child_name": "pytest tsv container action plate",
+            "child_content_type": "content/gdna/generic/1.0",
+        },
+    )
+    assert tsv_validation.status_code == 200, tsv_validation.text
+    tsv_payload = tsv_validation.json()
+    assert tsv_payload["valid"] is True
+    assert tsv_payload["planned"][0]["create_type"] == "container/plate/96-well/1.0"
+    assert tsv_payload["planned"][0]["target_well"] == "B2"
+
+    execution = client.post(
+        "/api/v1/container-actions/execute",
+        json={"rows": f"{tube_euid},CREATE.container/plate/96-well/1.0,A1\n"},
+    )
+    assert execution.status_code == 400, execution.text
+    assert "operation_type is required" in execution.text
+
+    class FakeLabActionsService:
+        def __init__(self):
+            self.closed = False
+
+        def create_lab_set(self, request):
+            return {
+                "set_euid": "Z-SET-CONTAINER-ACTION",
+                "members": request.members,
+                "external_members": request.external_members,
+            }
+
+        def close(self):
+            self.closed = True
+
+    fake_service = FakeLabActionsService()
+    monkeypatch.setattr(
+        container_actions_api,
+        "_service_for_user",
+        lambda user: fake_service,
+    )
+
+    explicit = client.post(
+        "/api/v1/container-actions/execute",
+        json={
+            "rows": f"{tube_euid},CREATE.set/run-set/generic/1.01,A1\n",
+            "operation_type": "lab_set",
+            "operation_payload": {
+                "name": "pytest container action set",
+                "members": [tube_euid],
+                "metadata": {"source": "container-actions-test"},
+            },
+        },
+    )
+    assert explicit.status_code == 200, explicit.text
+    executed = explicit.json()
+    assert executed["operation_type"] == "lab_set"
+    assert executed["validation"]["row_count"] == 1
+    assert executed["result"]["set_euid"]
+    assert executed["result"]["members"] == [tube_euid]
+    assert fake_service.closed is True
+
+
 def test_lab_actions_validation_and_ont_samplesheet_download() -> None:
     client = _client()
     invalid = client.post(
@@ -326,6 +420,20 @@ def test_lab_actions_gui_renders_wizard() -> None:
     assert "Download ${platform} sample sheet" in html
 
 
+def test_container_actions_gui_renders_dedicated_api_backed_page() -> None:
+    client = _client()
+    response = client.get("/container-actions")
+    assert response.status_code == 200, response.text
+    html = response.text
+    assert "Container Actions" in html
+    assert "/api/v1/container-actions/validate" in html
+    assert "/api/v1/container-actions/execute" in html
+    assert 'data-testid="bloom-container-action-rows"' in html
+    assert 'data-testid="bloom-container-action-operation"' in html
+    assert 'data-testid="bloom-container-action-payload"' in html
+    assert "Lab Actions" not in html.partition("")[0]
+
+
 def test_directed_extraction_into_existing_plate_with_quant_and_reuse_guard() -> None:
     client = _client()
     existing_plate_euid = _create_plate(client, name="pytest existing extraction plate")

From b096f1464047717db8a97ef68b8d836289762186 Mon Sep 17 00:00:00 2001
From: John Major 
Date: Fri, 19 Jun 2026 11:42:02 -0700
Subject: [PATCH 45/47] Pin TapDB 9.0.9

---
 README.md                        | 2 +-
 pyproject.toml                   | 2 +-
 tests/test_packaging_metadata.py | 2 +-
 uv.lock                          | 6 +++---
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 24a494e..62dd596 100644
--- a/README.md
+++ b/README.md
@@ -21,7 +21,7 @@
 
 Bloom is the LSMC internal material and container graph service. It owns laboratory containers, materials/content, equipment, lineage, recursive template creation, search, and graph views. Atlas owns orders and customer-facing accession context; Bloom owns the physical/material execution graph.
 
-Current Dayhoff pin: `7.0.20`. Current TapDB dependency: `daylily-tapdb @ ...@9.0.6`.
+Current Dayhoff pin: `7.0.22`. Current TapDB dependency: `daylily-tapdb @ ...@9.0.9`.
 
 Bloom is internal-only in Dayhoff exposure policy. It must be reachable only through approved LSMC networks and Dayhoff-generated service credentials.
 
diff --git a/pyproject.toml b/pyproject.toml
index f6171e5..6a6225e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,7 +28,7 @@ license = {text = "MIT"}
 requires-python = ">=3.12"
 dependencies = [
     "cli-core-yo==2.1.1",
-    "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.6",
+    "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.9",
     "daylily-auth-cognito==2.1.5",
     "IPython>=8.18.1",
     "bandit[toml]>=1.8.0",
diff --git a/tests/test_packaging_metadata.py b/tests/test_packaging_metadata.py
index 63c5e79..6051fbf 100644
--- a/tests/test_packaging_metadata.py
+++ b/tests/test_packaging_metadata.py
@@ -15,7 +15,7 @@ def test_project_dependencies_pin_release_train_versions() -> None:
 
     assert "cli-core-yo==2.1.1" in dependencies
     assert "daylily-auth-cognito==2.1.5" in dependencies
-    assert "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.6" in dependencies
+    assert "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.9" in dependencies
     assert "IPython>=8.18.1" in dependencies
     assert "psycopg2-binary==2.9.12" in dependencies
     assert not any(str(dep).startswith("zebra-day") for dep in dependencies)
diff --git a/uv.lock b/uv.lock
index 74ffb0e..f1b5a96 100644
--- a/uv.lock
+++ b/uv.lock
@@ -200,7 +200,7 @@ requires-dist = [
     { name = "cli-core-yo", specifier = "==2.1.1" },
     { name = "daylily-auth-cognito", specifier = "==2.1.5" },
     { name = "daylily-carrier-tracking", specifier = "==0.5.1" },
-    { name = "daylily-tapdb", git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.6" },
+    { name = "daylily-tapdb", git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.9" },
     { name = "djlint" },
     { name = "fastapi", specifier = ">=0.110.0" },
     { name = "httpx", specifier = ">=0.27.2" },
@@ -704,8 +704,8 @@ wheels = [
 
 [[package]]
 name = "daylily-tapdb"
-version = "9.0.6"
-source = { git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.6#ea195137638d1cc49b4499c9bf778c57b6d70d9b" }
+version = "9.0.9"
+source = { git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.9#52d5f498dc4751b7e42d346bee2811a14080e5a5" }
 dependencies = [
     { name = "cli-core-yo" },
     { name = "jsonschema" },

From e9961c942a1b69b35e63163eb48167bd8fee5641 Mon Sep 17 00:00:00 2001
From: John Major 
Date: Fri, 19 Jun 2026 12:14:06 -0700
Subject: [PATCH 46/47] Ignore TapDB generic set prefix in Bloom seeding

---
 bloom_lims/cli/db.py     | 2 +-
 tests/support/runtime.py | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/bloom_lims/cli/db.py b/bloom_lims/cli/db.py
index dd8859a..6117666 100644
--- a/bloom_lims/cli/db.py
+++ b/bloom_lims/cli/db.py
@@ -48,7 +48,7 @@
 db_app = typer.Typer(help="Database management commands routed through daylily-tapdb.")
 console = Console()
 
-_TAPDB_CORE_TEMPLATE_PREFIXES = {"ADT", "EDG", "GVR", "MSG", "SYS", "TPX", "XRF"}
+_TAPDB_CORE_TEMPLATE_PREFIXES = {"ADT", "EDG", "GSE", "GVR", "MSG", "SYS", "TPX", "XRF"}
 _IDENTITY_PREFIXES: dict[str, str] = {
     "generic_template": GENERIC_TEMPLATE_PREFIX,
     "generic_instance_lineage": GENERIC_INSTANCE_LINEAGE_PREFIX,
diff --git a/tests/support/runtime.py b/tests/support/runtime.py
index 46dd1c1..fbc274f 100644
--- a/tests/support/runtime.py
+++ b/tests/support/runtime.py
@@ -56,6 +56,7 @@
 _TAPDB_CORE_PREFIX_OWNERSHIP = {
     "ADT",
     "EDG",
+    "GSE",
     "GVR",
     "MSG",
     "SYS",

From 856f92186a04ba91cf1ba3d825d0522d9ca97c32 Mon Sep 17 00:00:00 2001
From: John Major 
Date: Wed, 1 Jul 2026 17:19:44 -0700
Subject: [PATCH 47/47] Release Bloom 8.0.0 with TapDB 9.0.10

---
 README.md                                     |   2 +-
 bloom_lims/ai_agent_access.py                 |  28 ++-
 bloom_lims/api/v1/__init__.py                 |   2 +-
 bloom_lims/api/v1/auth.py                     |  25 +-
 bloom_lims/api/v1/container_actions.py        |  23 +-
 bloom_lims/api/v1/lab_actions.py              |   8 +-
 bloom_lims/cli/db.py                          |  24 +-
 bloom_lims/domain/beta_actions.py             |   4 +-
 bloom_lims/domain/beta_lab_refs.py            |  18 +-
 bloom_lims/domain/beta_lab_stages.py          |   4 +-
 bloom_lims/domain/containers.py               |  14 +-
 bloom_lims/domain/execution_actions.py        |   2 +-
 bloom_lims/domain/execution_queue.py          |  40 ++--
 bloom_lims/domain/lab_action_spreadsheets.py  |   3 +-
 bloom_lims/domain/lab_actions.py              | 213 +++++++++++++-----
 bloom_lims/etc/prefix_ownership_registry.json |   3 +
 bloom_lims/gui/actions.py                     |  15 +-
 bloom_lims/integrations/tapdb_mount.py        |   4 +-
 bloom_lims/schemas/beta_lab.py                |  10 +-
 bloom_lims/schemas/lab_actions.py             |   4 +-
 bloom_lims/schemas/objects.py                 |  70 ++++--
 bloom_lims/tapdb_metrics.py                   |   4 +-
 container_tests/test_container_runtime.py     |   7 +-
 pyproject.toml                                |   3 +-
 tests/test_action_button_template_safety.py   |  21 +-
 tests/test_action_schema_hydration.py         |   7 +-
 tests/test_anomalies.py                       |   8 +-
 tests/test_beta_lab_schema.py                 |   4 +-
 tests/test_beta_modern_action_system.py       |  56 ++++-
 tests/test_cli_db_command_paths.py            |  25 +-
 tests/test_config_runtime.py                  |   7 +-
 tests/test_core_validation.py                 |  85 ++++---
 tests/test_cytoscape_dag.py                   | 100 ++++----
 tests/test_domain_workflows_helpers.py        | 100 ++++++--
 tests/test_lab_actions_api.py                 |  28 ++-
 tests/test_packaging_metadata.py              |  10 +-
 tests/test_queue_flow.py                      |   5 +-
 tests/test_route_coverage_gaps_api.py         |  19 +-
 tests/test_route_coverage_gaps_gui.py         |  20 +-
 tests/test_sequencing_run_contract.py         |   1 -
 .../test_template_instantiation_recursion.py  |  16 +-
 uv.lock                                       |  17 +-
 42 files changed, 735 insertions(+), 324 deletions(-)

diff --git a/README.md b/README.md
index 62dd596..6e0ea7c 100644
--- a/README.md
+++ b/README.md
@@ -21,7 +21,7 @@
 
 Bloom is the LSMC internal material and container graph service. It owns laboratory containers, materials/content, equipment, lineage, recursive template creation, search, and graph views. Atlas owns orders and customer-facing accession context; Bloom owns the physical/material execution graph.
 
-Current Dayhoff pin: `7.0.22`. Current TapDB dependency: `daylily-tapdb @ ...@9.0.9`.
+Current Dayhoff pin: `8.0.0`. Current TapDB dependency: `daylily-tapdb @ ...@9.0.10`.
 
 Bloom is internal-only in Dayhoff exposure policy. It must be reachable only through approved LSMC networks and Dayhoff-generated service credentials.
 
diff --git a/bloom_lims/ai_agent_access.py b/bloom_lims/ai_agent_access.py
index 8639e8b..2d18822 100644
--- a/bloom_lims/ai_agent_access.py
+++ b/bloom_lims/ai_agent_access.py
@@ -78,9 +78,13 @@ def _endpoint_id_for_request(method: str, path: str) -> str:
     resolved_method = str(method or "").upper()
     resolved_path = str(path or "").split("?", 1)[0].rstrip("/") or "/"
     for spec in ENDPOINT_CATALOG:
-        if spec.method == resolved_method and _template_matches(spec.path_template, resolved_path):
+        if spec.method == resolved_method and _template_matches(
+            spec.path_template, resolved_path
+        ):
             return spec.endpoint_id
-    raise AgentTokenError("AI-agent token is not authorized for this endpoint", status_code=403)
+    raise AgentTokenError(
+        "AI-agent token is not authorized for this endpoint", status_code=403
+    )
 
 
 def _parse_expiry(value: str) -> datetime:
@@ -95,15 +99,21 @@ def _parse_expiry(value: str) -> datetime:
 
 def _load_grants(path: Path) -> list[dict[str, Any]]:
     if not path.is_absolute():
-        raise AgentTokenError("AI-agent grant store path must be absolute", status_code=500)
+        raise AgentTokenError(
+            "AI-agent grant store path must be absolute", status_code=500
+        )
     if not path.exists():
         raise AgentTokenError("AI-agent grant store is missing", status_code=500)
     try:
         payload = json.loads(path.read_text(encoding="utf-8"))
     except json.JSONDecodeError as exc:
-        raise AgentTokenError("AI-agent grant store is malformed", status_code=500) from exc
+        raise AgentTokenError(
+            "AI-agent grant store is malformed", status_code=500
+        ) from exc
     if not isinstance(payload, dict) or not isinstance(payload.get("tokens"), list):
-        raise AgentTokenError("AI-agent grant store must contain a tokens list", status_code=500)
+        raise AgentTokenError(
+            "AI-agent grant store must contain a tokens list", status_code=500
+        )
     return [record for record in payload["tokens"] if isinstance(record, dict)]
 
 
@@ -119,7 +129,9 @@ def validate_ai_agent_request(request: Request, token: str) -> ValidatedAgentAcc
     endpoint_id = _endpoint_id_for_request(request.method, request.url.path)
     token_digest = hashlib.sha256(token.encode("utf-8")).hexdigest()
     for record in _load_grants(Path(raw_path)):
-        if not secrets.compare_digest(str(record.get("token_hash") or ""), token_digest):
+        if not secrets.compare_digest(
+            str(record.get("token_hash") or ""), token_digest
+        ):
             continue
         if record.get("revoked_at"):
             raise AgentTokenError("AI-agent token has been revoked")
@@ -128,7 +140,9 @@ def validate_ai_agent_request(request: Request, token: str) -> ValidatedAgentAcc
             raise AgentTokenError("AI-agent token has expired")
         endpoint_ids = [str(item) for item in record.get("endpoint_ids") or []]
         if endpoint_id not in endpoint_ids:
-            raise AgentTokenError("AI-agent token is not authorized for this endpoint", status_code=403)
+            raise AgentTokenError(
+                "AI-agent token is not authorized for this endpoint", status_code=403
+            )
         validated = ValidatedAgentAccess(
             token_id=str(record.get("token_id") or ""),
             agent_id=str(record.get("agent_id") or ""),
diff --git a/bloom_lims/api/v1/__init__.py b/bloom_lims/api/v1/__init__.py
index 7fd8888..5c8dd61 100644
--- a/bloom_lims/api/v1/__init__.py
+++ b/bloom_lims/api/v1/__init__.py
@@ -20,8 +20,8 @@
 from .auth import router as auth_router
 from .batch import router as batch_router
 from .beta_lab import router as beta_lab_router
-from .containers import router as containers_router
 from .container_actions import router as container_actions_router
+from .containers import router as containers_router
 from .content import router as content_router
 from .equipment import router as equipment_router
 from .execution_queue import router as execution_queue_router
diff --git a/bloom_lims/api/v1/auth.py b/bloom_lims/api/v1/auth.py
index f00a054..e0a32e7 100644
--- a/bloom_lims/api/v1/auth.py
+++ b/bloom_lims/api/v1/auth.py
@@ -25,9 +25,13 @@ def _broker_preferences_contract(email: str) -> tuple[str, dict[str, str]]:
     token = str(os.environ.get("LSMC_AUTH_BROKER_SERVICE_TOKEN") or "").strip()
     service_id = str(os.environ.get("LSMC_AUTH_BROKER_SERVICE_ID") or "bloom").strip()
     if not raw_url:
-        raise HTTPException(status_code=503, detail="Broker user preferences URL is not configured")
+        raise HTTPException(
+            status_code=503, detail="Broker user preferences URL is not configured"
+        )
     if not token:
-        raise HTTPException(status_code=503, detail="Broker service token is not configured")
+        raise HTTPException(
+            status_code=503, detail="Broker service token is not configured"
+        )
     if "{email}" not in raw_url:
         raise HTTPException(
             status_code=503,
@@ -58,7 +62,9 @@ async def get_current_user(user: APIUser = Depends(require_api_auth)):
 @preferences_router.get("/me/preferences")
 async def current_user_preferences(user: APIUser = Depends(require_api_auth)):
     if not user.email:
-        raise HTTPException(status_code=400, detail="Authenticated user email is required")
+        raise HTTPException(
+            status_code=400, detail="Authenticated user email is required"
+        )
     url, headers = _broker_preferences_contract(user.email)
     with httpx.Client(timeout=5.0) as client:
         response = client.get(url, headers=headers)
@@ -73,7 +79,9 @@ async def update_current_user_preferences(
     user: APIUser = Depends(require_api_auth),
 ):
     if not user.email:
-        raise HTTPException(status_code=400, detail="Authenticated user email is required")
+        raise HTTPException(
+            status_code=400, detail="Authenticated user email is required"
+        )
     payload = await request.json()
     theme = str(payload.get("theme") or "").strip()
     if theme and theme not in THEME_NAMES:
@@ -81,9 +89,14 @@ async def update_current_user_preferences(
     service_themes = payload.get("service_themes")
     if service_themes is not None:
         if not isinstance(service_themes, dict):
-            raise HTTPException(status_code=400, detail="service_themes must be an object")
+            raise HTTPException(
+                status_code=400, detail="service_themes must be an object"
+            )
         for service_theme in service_themes.values():
-            if service_theme is not None and str(service_theme).strip() not in THEME_NAMES:
+            if (
+                service_theme is not None
+                and str(service_theme).strip() not in THEME_NAMES
+            ):
                 raise HTTPException(status_code=400, detail="Unknown theme")
     forward_payload = {}
     if "theme" in payload:
diff --git a/bloom_lims/api/v1/container_actions.py b/bloom_lims/api/v1/container_actions.py
index 440324f..01cc548 100644
--- a/bloom_lims/api/v1/container_actions.py
+++ b/bloom_lims/api/v1/container_actions.py
@@ -10,7 +10,6 @@
 from pydantic import BaseModel, Field, ValidationError
 from sqlalchemy import select
 
-from bloom_lims.tapdb_adapter import BLOOMdb3, generic_instance
 from bloom_lims.domain.lab_actions import LabActionsService
 from bloom_lims.schemas.lab_actions import (
     ExtractionPlateRequest,
@@ -22,6 +21,7 @@
     SeqLibraryPoolRequest,
     SeqRunSetRequest,
 )
+from bloom_lims.tapdb_adapter import BLOOMdb3, generic_instance
 
 from .dependencies import APIUser, require_write
 
@@ -76,8 +76,12 @@ def _split_source(value: str) -> tuple[str, str | None]:
     return euid, well
 
 
-def _normalize_record(row: dict[str, Any], default_target: str | None) -> dict[str, Any]:
-    source = row.get("source") or row.get("source_euid") or row.get("euid") or row.get("0")
+def _normalize_record(
+    row: dict[str, Any], default_target: str | None
+) -> dict[str, Any]:
+    source = (
+        row.get("source") or row.get("source_euid") or row.get("euid") or row.get("0")
+    )
     target = (
         row.get("target")
         or row.get("target_container_euid")
@@ -159,7 +163,10 @@ async def validate_container_action(
 ):
     try:
         planned = _parse_rows(payload)
-        source_types = {row["source_euid"]: _object_kind(row["source_euid"], user) for row in planned}
+        source_types = {
+            row["source_euid"]: _object_kind(row["source_euid"], user)
+            for row in planned
+        }
         target_types = {
             row["target_euid"]: _object_kind(row["target_euid"], user)
             for row in planned
@@ -232,9 +239,13 @@ async def execute_container_action(
                 SeqRunSetRequest.model_validate(operation_payload)
             )
         elif payload.operation_type == "lab_set":
-            result = service.create_lab_set(LabSetRequest.model_validate(operation_payload))
+            result = service.create_lab_set(
+                LabSetRequest.model_validate(operation_payload)
+            )
         elif payload.operation_type == "print_euids":
-            result = service.print_euids(PrintEuidRequest.model_validate(operation_payload))
+            result = service.print_euids(
+                PrintEuidRequest.model_validate(operation_payload)
+            )
         else:  # pragma: no cover - Literal validation should prevent this.
             raise HTTPException(status_code=400, detail="Unsupported operation_type")
         return {
diff --git a/bloom_lims/api/v1/lab_actions.py b/bloom_lims/api/v1/lab_actions.py
index 99191af..4698baa 100644
--- a/bloom_lims/api/v1/lab_actions.py
+++ b/bloom_lims/api/v1/lab_actions.py
@@ -177,13 +177,13 @@ async def download_seq_run_sample_sheet(
 ):
     service = _service_for_user(user)
     try:
-        content, filename, media_type = service.sequencing_sample_sheet_download(set_euid)
+        content, filename, media_type = service.sequencing_sample_sheet_download(
+            set_euid
+        )
         return PlainTextResponse(
             content,
             media_type=media_type,
-            headers={
-                "Content-Disposition": f'attachment; filename="{filename}"'
-            },
+            headers={"Content-Disposition": f'attachment; filename="{filename}"'},
         )
     except Exception as exc:
         _raise_http(exc)
diff --git a/bloom_lims/cli/db.py b/bloom_lims/cli/db.py
index 6117666..ae1ce71 100644
--- a/bloom_lims/cli/db.py
+++ b/bloom_lims/cli/db.py
@@ -383,6 +383,20 @@ def _retire_obsolete_template_variants(
     domain_code: str,
 ) -> int:
     current = _active_template_categories_by_semantic_key(templates)
+    current_semantic_types = {
+        (
+            str((template.get("json_addl") or {}).get("semantic_category") or "")
+            .strip()
+            .lower(),
+            str(template.get("type") or "").strip(),
+        )
+        for template in templates
+        if isinstance(template.get("json_addl"), dict)
+        and str(
+            (template.get("json_addl") or {}).get("semantic_category") or ""
+        ).strip()
+        and str(template.get("type") or "").strip()
+    }
     current_prefixes = {
         str(template.get("instance_prefix") or "").strip().upper()
         for template in templates
@@ -411,18 +425,16 @@ def _retire_obsolete_template_variants(
             )
             expected_category = current.get(key)
             actual_category = str(row.category or "").strip().upper()
-            semantic_category = template_semantic_category(row).strip().upper()
-            if semantic_category and actual_category != semantic_category:
-                row.is_deleted = True
-                row.bstatus = "retired"
-                retired += 1
-                continue
             if actual_category in current_prefixes:
                 row.is_deleted = True
                 row.bstatus = "retired"
                 retired += 1
                 continue
             if expected_category is None:
+                if (key[0], key[1]) in current_semantic_types:
+                    row.is_deleted = True
+                    row.bstatus = "retired"
+                    retired += 1
                 continue
             if actual_category == expected_category:
                 continue
diff --git a/bloom_lims/domain/beta_actions.py b/bloom_lims/domain/beta_actions.py
index 573b544..3ccd7fe 100644
--- a/bloom_lims/domain/beta_actions.py
+++ b/bloom_lims/domain/beta_actions.py
@@ -187,9 +187,7 @@ def record(
         return action_record
 
     def _ensure_action_template(self, action_key: str) -> generic_template:
-        template_code = (
-            f"{BETA_ACTION_TEMPLATE_PREFIX}/{BETA_ACTION_GROUP}/{action_key}/1.0/"
-        )
+        template_code = f"action/{BETA_ACTION_GROUP}/{action_key}/1.0/"
         return require_seeded_template(
             self.session,
             template_code,
diff --git a/bloom_lims/domain/beta_lab_refs.py b/bloom_lims/domain/beta_lab_refs.py
index a7890fb..71c2112 100644
--- a/bloom_lims/domain/beta_lab_refs.py
+++ b/bloom_lims/domain/beta_lab_refs.py
@@ -172,9 +172,7 @@ def _fulfillment_item_refs_for_instance(self, instance) -> list[dict[str, str]]:
             ).strip()
             atlas_tenant_id = str(payload.get("atlas_tenant_id") or "").strip()
             atlas_trf_euid = str(
-                payload.get("atlas_trf_euid")
-                or payload.get("atlas_order_euid")
-                or ""
+                payload.get("atlas_trf_euid") or payload.get("atlas_order_euid") or ""
             ).strip()
             if not (
                 fulfillment_item_euid
@@ -195,8 +193,7 @@ def _fulfillment_item_refs_for_instance(self, instance) -> list[dict[str, str]]:
                     payload.get("atlas_order_test_euid") or atlas_test_euid
                 ).strip(),
                 "atlas_fulfillment_slot_euid": str(
-                    payload.get("atlas_fulfillment_slot_euid")
-                    or fulfillment_item_euid
+                    payload.get("atlas_fulfillment_slot_euid") or fulfillment_item_euid
                 ).strip(),
             }
         return list(refs.values())
@@ -366,7 +363,9 @@ def _replace_fulfillment_item_references(
         atlas_tenant_id = str(atlas_context.get("atlas_tenant_id") or "").strip()
         atlas_trf_euid = str(atlas_context.get("atlas_trf_euid") or "").strip()
         atlas_order_euid = str(
-            atlas_context.get("atlas_order_euid") or atlas_context.get("order_euid") or ""
+            atlas_context.get("atlas_order_euid")
+            or atlas_context.get("order_euid")
+            or ""
         ).strip()
         fulfillment_items = list(atlas_context.get("fulfillment_items") or [])
         for fulfillment_slot in list(atlas_context.get("fulfillment_slots") or []):
@@ -464,8 +463,7 @@ def _replace_fulfillment_item_references(
                     object_evidence(ref_obj.euid, role="atlas_reference_link"),
                 ],
                 correlation_id=(
-                    f"SLOT_SATISFIED_BY:{atlas_fulfillment_slot_euid}:"
-                    f"{instance.euid}"
+                    f"SLOT_SATISFIED_BY:{atlas_fulfillment_slot_euid}:{instance.euid}"
                 ),
                 causation_id=(
                     f"bloom:atlas_fulfillment_reference:"
@@ -484,7 +482,9 @@ def _replace_container_entity_references(
     ) -> None:
         atlas_tenant_id = str(atlas_context.get("atlas_tenant_id") or "").strip()
         atlas_order_euid = str(
-            atlas_context.get("atlas_order_euid") or atlas_context.get("order_euid") or ""
+            atlas_context.get("atlas_order_euid")
+            or atlas_context.get("order_euid")
+            or ""
         ).strip()
         atlas_order_test_euid = str(
             atlas_context.get("atlas_order_test_euid")
diff --git a/bloom_lims/domain/beta_lab_stages.py b/bloom_lims/domain/beta_lab_stages.py
index 971a736..5b8969f 100644
--- a/bloom_lims/domain/beta_lab_stages.py
+++ b/bloom_lims/domain/beta_lab_stages.py
@@ -409,9 +409,7 @@ def record_post_extract_qc(
                 "idempotency_key": idempotency_key or "",
                 "occurred_at": self._timestamp(),
             },
-            template_code=self.DATA_TEMPLATE_BY_BETA_KIND.get(
-                "post_extract_qc_result"
-            ),
+            template_code=self.DATA_TEMPLATE_BY_BETA_KIND.get("post_extract_qc_result"),
         )
         if payload.quant_artifact_euid:
             qc_props = self._props(qc_record)
diff --git a/bloom_lims/domain/containers.py b/bloom_lims/domain/containers.py
index 8e63a2b..dfee826 100644
--- a/bloom_lims/domain/containers.py
+++ b/bloom_lims/domain/containers.py
@@ -18,7 +18,9 @@
 
 class BloomContainer(BloomObj):
     def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
-        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
+        super().__init__(
+            bdb, is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex
+        )
 
     def create_empty_container(self, template_euid):
         return self.create_instances(template_euid)
@@ -56,12 +58,16 @@ def unlink_content(self, container_euid, content_euid):
                 lineage.is_deleted = True
                 self.session.commit()
                 return
-        raise Exception(f"Content {content_euid} not found in container {container_euid}")
+        raise Exception(
+            f"Content {content_euid} not found in container {container_euid}"
+        )
 
 
 class BloomContainerPlate(BloomContainer):
     def __init__(self, bdb, is_deleted=False, cfg_printers=False, cfg_fedex=False):
-        super().__init__(bdb,is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex)
+        super().__init__(
+            bdb, is_deleted=is_deleted, cfg_printers=cfg_printers, cfg_fedex=cfg_fedex
+        )
 
     def create_empty_plate(self, template_euid):
         return self.create_instances(template_euid)
@@ -119,8 +125,6 @@ def organize_wells(self, wells, parent_container):
         return matrix
 
 
-
-
 __all__ = [
     "BloomContainer",
     "BloomContainerPlate",
diff --git a/bloom_lims/domain/execution_actions.py b/bloom_lims/domain/execution_actions.py
index f1f7b9f..27896a0 100644
--- a/bloom_lims/domain/execution_actions.py
+++ b/bloom_lims/domain/execution_actions.py
@@ -228,7 +228,7 @@ def record(
         return action_record
 
     def _ensure_action_template(self, action_key: str) -> generic_template:
-        template_code = f"{EXECUTION_ACTION_TEMPLATE_PREFIX}/{EXECUTION_ACTION_GROUP}/{action_key}/1.0/"
+        template_code = f"action/{EXECUTION_ACTION_GROUP}/{action_key}/1.0/"
         return require_seeded_template(
             self.session,
             template_code,
diff --git a/bloom_lims/domain/execution_queue.py b/bloom_lims/domain/execution_queue.py
index bdf0f6e..8b12f37 100644
--- a/bloom_lims/domain/execution_queue.py
+++ b/bloom_lims/domain/execution_queue.py
@@ -130,7 +130,7 @@ class ExecutionQueueService:
             "dispatch_priority": 100,
             "subject_template_codes": [
                 "container/tube/tube-generic-10ml/1.0",
-                "material/specimen/blood-whole/1.0",
+                "content/specimen/blood-whole/1.0",
             ],
             "required_worker_capabilities": ["wetlab.extraction"],
         },
@@ -139,7 +139,7 @@ class ExecutionQueueService:
             "dispatch_priority": 90,
             "subject_template_codes": [
                 "container/tube/tube-generic-10ml/1.0",
-                "material/specimen/blood-whole/1.0",
+                "content/specimen/blood-whole/1.0",
             ],
             "required_worker_capabilities": ["wetlab.extraction"],
         },
@@ -147,8 +147,8 @@ class ExecutionQueueService:
             "display_name": "Post-Extract QC",
             "dispatch_priority": 100,
             "subject_template_codes": [
-                "material/sample/cfdna/1.0",
-                "material/sample/gdna/1.0",
+                "content/sample/cfdna/1.0",
+                "content/sample/gdna/1.0",
             ],
             "required_worker_capabilities": ["wetlab.post_extract_qc"],
         },
@@ -156,8 +156,8 @@ class ExecutionQueueService:
             "display_name": "Illumina Library Prep",
             "dispatch_priority": 100,
             "subject_template_codes": [
-                "material/sample/cfdna/1.0",
-                "material/sample/gdna/1.0",
+                "content/sample/cfdna/1.0",
+                "content/sample/gdna/1.0",
             ],
             "required_worker_capabilities": ["wetlab.library_prep", "platform.ILMN"],
         },
@@ -165,7 +165,7 @@ class ExecutionQueueService:
             "display_name": "Illumina Library QC",
             "dispatch_priority": 100,
             "subject_template_codes": [
-                "material/sample/sequencing-library/1.0",
+                "content/sample/sequencing-library/1.0",
             ],
             "required_worker_capabilities": ["wetlab.library_qc", "platform.ILMN"],
         },
@@ -173,8 +173,8 @@ class ExecutionQueueService:
             "display_name": "ONT Library Prep",
             "dispatch_priority": 100,
             "subject_template_codes": [
-                "material/sample/cfdna/1.0",
-                "material/sample/gdna/1.0",
+                "content/sample/cfdna/1.0",
+                "content/sample/gdna/1.0",
             ],
             "required_worker_capabilities": ["wetlab.library_prep", "platform.ONT"],
         },
@@ -183,7 +183,7 @@ class ExecutionQueueService:
             "dispatch_priority": 100,
             "subject_template_codes": [
                 "data/operation/library-prep/1.0",
-                "material/sample/sequencing-library/1.0",
+                "content/sample/sequencing-library/1.0",
             ],
             "required_worker_capabilities": ["wetlab.pooling", "platform.ILMN"],
         },
@@ -192,28 +192,28 @@ class ExecutionQueueService:
             "dispatch_priority": 100,
             "subject_template_codes": [
                 "data/operation/library-prep/1.0",
-                "material/sample/sequencing-library/1.0",
+                "content/sample/sequencing-library/1.0",
             ],
             "required_worker_capabilities": ["wetlab.pooling", "platform.ONT"],
         },
         "ilmn_start_seq_run": {
             "display_name": "Illumina Start Run",
             "dispatch_priority": 100,
-            "subject_template_codes": ["material/pool/sequencing-library/1.0"],
+            "subject_template_codes": ["content/pool/sequencing-library/1.0"],
             "required_worker_capabilities": ["wetlab.run_start", "platform.ILMN"],
         },
         "ont_start_seq_run": {
             "display_name": "ONT Start Run",
             "dispatch_priority": 100,
-            "subject_template_codes": ["material/pool/sequencing-library/1.0"],
+            "subject_template_codes": ["content/pool/sequencing-library/1.0"],
             "required_worker_capabilities": ["wetlab.run_start", "platform.ONT"],
         },
         "post_extract_exception": {
             "display_name": "Post-Extract QC Exception",
             "dispatch_priority": 10,
             "subject_template_codes": [
-                "material/sample/cfdna/1.0",
-                "material/sample/gdna/1.0",
+                "content/sample/cfdna/1.0",
+                "content/sample/gdna/1.0",
             ],
             "required_worker_capabilities": ["wetlab.exception_review"],
         },
@@ -221,7 +221,7 @@ class ExecutionQueueService:
             "display_name": "Illumina Library QC Exception",
             "dispatch_priority": 10,
             "subject_template_codes": [
-                "material/sample/sequencing-library/1.0",
+                "content/sample/sequencing-library/1.0",
             ],
             "required_worker_capabilities": [
                 "wetlab.exception_review",
@@ -1480,7 +1480,9 @@ def current_queue_for_instance(self, instance) -> str | None:
         if queue_key:
             return queue_key
         category = instance_semantic_category(instance)
-        parent_relationship = "contains" if category == "container" else "HOLDS_MATERIAL"
+        parent_relationship = (
+            "contains" if category == "container" else "HOLDS_MATERIAL"
+        )
         for lineage in get_child_lineages(instance):
             if lineage.is_deleted or lineage.relationship_type != parent_relationship:
                 continue
@@ -2053,7 +2055,9 @@ def _is_visible_in_queue(self, subject, queue, now: datetime) -> bool:
         if subject.uid in visible_uids:
             return True
         category = instance_semantic_category(subject)
-        parent_relationship = "contains" if category == "container" else "HOLDS_MATERIAL"
+        parent_relationship = (
+            "contains" if category == "container" else "HOLDS_MATERIAL"
+        )
         for lineage in get_child_lineages(subject):
             if lineage.is_deleted or lineage.relationship_type != parent_relationship:
                 continue
diff --git a/bloom_lims/domain/lab_action_spreadsheets.py b/bloom_lims/domain/lab_action_spreadsheets.py
index e025cc9..fdf5587 100644
--- a/bloom_lims/domain/lab_action_spreadsheets.py
+++ b/bloom_lims/domain/lab_action_spreadsheets.py
@@ -9,7 +9,8 @@
 from dataclasses import dataclass
 from pathlib import PurePosixPath
 from typing import Any
-from xml.etree import ElementTree
+
+from defusedxml import ElementTree
 
 
 @dataclass(frozen=True)
diff --git a/bloom_lims/domain/lab_actions.py b/bloom_lims/domain/lab_actions.py
index 6adb276..a07cad2 100644
--- a/bloom_lims/domain/lab_actions.py
+++ b/bloom_lims/domain/lab_actions.py
@@ -237,13 +237,18 @@ def _normalize_assignments(
                 raise ValueError(f"duplicate destination well: {position}")
             seen_positions.add(position)
         if len(request.assignments) > MAX_EXTRACTION_TUBES:
-            raise ValueError(f"directed extraction accepts at most {MAX_EXTRACTION_TUBES} tubes")
+            raise ValueError(
+                f"directed extraction accepts at most {MAX_EXTRACTION_TUBES} tubes"
+            )
         return request.assignments
 
     def _create_or_get_extraction_plate(self, request: ExtractionPlateRequest):
         if request.plate_euid:
             plate = self._require(request.plate_euid)
-            if instance_semantic_category(plate) != "container" or plate.type != "plate":
+            if (
+                instance_semantic_category(plate) != "container"
+                or plate.type != "plate"
+            ):
                 raise ValueError(f"{request.plate_euid} is not a plate container")
             return plate
         return self._create_by_code(
@@ -303,7 +308,9 @@ def _well_for_qc_assignment(
         if assignment.source_well_euid:
             return self._require(assignment.source_well_euid)
         if not source_plate_euid:
-            raise ValueError("source_plate_euid is required when assignment uses row/col")
+            raise ValueError(
+                "source_plate_euid is required when assignment uses row/col"
+            )
         return self._well_from_plate_position(
             source_plate_euid, assignment.row, assignment.col
         )
@@ -311,7 +318,10 @@ def _well_for_qc_assignment(
     def _create_or_get_qc_plate(self, request: ExtractionQcPlateRequest):
         if request.qc_plate_euid:
             plate = self._require(request.qc_plate_euid)
-            if instance_semantic_category(plate) != "container" or plate.type != "plate":
+            if (
+                instance_semantic_category(plate) != "container"
+                or plate.type != "plate"
+            ):
                 raise ValueError(f"{request.qc_plate_euid} is not a plate container")
             return plate, []
         plate = self._create_by_code(
@@ -369,9 +379,7 @@ def add_lab_set_members(
     ) -> dict[str, Any]:
         run_set = self._require(set_euid)
         props = self._props(run_set)
-        members = list(
-            dict.fromkeys([*props.get("members", []), *request.members])
-        )
+        members = list(dict.fromkeys([*props.get("members", []), *request.members]))
         external_members = list(
             dict.fromkeys(
                 [*props.get("external_members", []), *request.external_members]
@@ -511,13 +519,17 @@ def attach_plate_well_data(self, request: PlateWellDataRequest) -> dict[str, Any
         self.bdb.session.commit()
         sorted_plate_euids = sorted(plate_euids)
         return {
-            "plate_euid": sorted_plate_euids[0] if len(sorted_plate_euids) == 1 else None,
+            "plate_euid": sorted_plate_euids[0]
+            if len(sorted_plate_euids) == 1
+            else None,
             "plate_euids": sorted_plate_euids,
             "run_set_euid": run_set.euid if run_set is not None else None,
             "mappings": mappings,
         }
 
-    def create_extraction_plate(self, request: ExtractionPlateRequest) -> dict[str, Any]:
+    def create_extraction_plate(
+        self, request: ExtractionPlateRequest
+    ) -> dict[str, Any]:
         assignments = self._normalize_assignments(request)
         plate = self._create_or_get_extraction_plate(request)
         wells = self._plate_wells(plate)
@@ -600,7 +612,9 @@ def create_extraction_plate(self, request: ExtractionPlateRequest) -> dict[str,
             "mappings": [item.__dict__ for item in mappings],
         }
 
-    def create_seq_library_plate(self, request: SeqLibraryPlateRequest) -> dict[str, Any]:
+    def create_seq_library_plate(
+        self, request: SeqLibraryPlateRequest
+    ) -> dict[str, Any]:
         if request.mode == "plate_1_to_1":
             source_plate = self._require(request.source_plate_euid)
             source_wells = self._plate_wells(source_plate)
@@ -669,7 +683,9 @@ def create_seq_library_plate(self, request: SeqLibraryPlateRequest) -> dict[str,
                 source_role="source_material",
                 target_role="derived_material",
             )
-            self._create_lineage(source_well.euid, dest_well.euid, "library_source_well")
+            self._create_lineage(
+                source_well.euid, dest_well.euid, "library_source_well"
+            )
             if assignment.index_euid:
                 index = self._require(assignment.index_euid)
                 self._create_lineage(library.euid, index.euid, "uses_index")
@@ -688,7 +704,10 @@ def create_seq_library_plate(self, request: SeqLibraryPlateRequest) -> dict[str,
             requested=request.create_run_set,
             run_set=request.run_set,
             default_name=f"{plate.euid} library set",
-            member_euids=[plate.euid, *[item["library_content_euid"] for item in mappings]],
+            member_euids=[
+                plate.euid,
+                *[item["library_content_euid"] for item in mappings],
+            ],
         )
         self.bdb.session.commit()
         return {
@@ -754,7 +773,9 @@ def create_seq_library_pool(self, request: SeqLibraryPoolRequest) -> dict[str, A
                 target_role="derived_material",
             )
             if container is not None:
-                self._create_lineage(container.euid, pool_tube.euid, "pooled_from_container")
+                self._create_lineage(
+                    container.euid, pool_tube.euid, "pooled_from_container"
+                )
         run_set = self._run_set(
             requested=request.create_run_set,
             run_set=request.run_set,
@@ -802,7 +823,9 @@ def create_seq_run_set(self, request: SeqRunSetRequest) -> dict[str, Any]:
         self._create_lineage(run_set.euid, pool_tube.euid, "run_uses_pool")
         self._create_lineage(run_set.euid, pool_content.euid, "run_uses_pool")
         if request.instrument_euid:
-            self._create_lineage(run_set.euid, request.instrument_euid, "run_uses_instrument")
+            self._create_lineage(
+                run_set.euid, request.instrument_euid, "run_uses_instrument"
+            )
         for reagent_euid in request.reagent_euids:
             self._create_lineage(run_set.euid, reagent_euid, "run_uses_reagent")
         assignments = self._create_sequenced_library_assignments(
@@ -890,7 +913,9 @@ def plate_mapping_rows(self, plate_euid: str) -> list[dict[str, str]]:
             ]
             source_tubes = [
                 lineage.parent_instance.euid
-                for lineage in self._lineages_to_child(well, "extraction_source_container")
+                for lineage in self._lineages_to_child(
+                    well, "extraction_source_container"
+                )
             ]
             for content in well_contents or [None]:
                 parent_contents = []
@@ -911,7 +936,9 @@ def plate_mapping_rows(self, plate_euid: str) -> list[dict[str, str]]:
                         "well_euid": well.euid,
                         "well_row": row,
                         "well_col": col,
-                        "well_content_euid": content.euid if content is not None else "",
+                        "well_content_euid": content.euid
+                        if content is not None
+                        else "",
                         "parent_content_euid": "|".join(parent_contents),
                         "one_degree_parent_euids": "|".join(parent_contents),
                         "one_degree_child_euids": "|".join(child_euids),
@@ -958,7 +985,9 @@ def sequencing_sample_sheet(self, set_euid: str) -> str:
             source_specimen = (
                 [
                     lineage.parent_instance
-                    for lineage in self._lineages_to_child(source_material, "DERIVED_FROM")
+                    for lineage in self._lineages_to_child(
+                        source_material, "DERIVED_FROM"
+                    )
                 ][0]
                 if source_material is not None
                 and self._lineages_to_child(source_material, "DERIVED_FROM")
@@ -985,12 +1014,16 @@ def sequencing_sample_sheet(self, set_euid: str) -> str:
                 }
             )
         if platform == "ONT":
-            return self._ont_sample_sheet(run_set=run_set, props=props, data_rows=data_rows)
+            return self._ont_sample_sheet(
+                run_set=run_set, props=props, data_rows=data_rows
+            )
         if platform != "ILMN":
             raise ValueError(
                 f"Sample sheet download is implemented for ILMN and ONT, not {platform or 'unknown'}"
             )
-        return self._illumina_sample_sheet(run_set=run_set, props=props, data_rows=data_rows)
+        return self._illumina_sample_sheet(
+            run_set=run_set, props=props, data_rows=data_rows
+        )
 
     def sequencing_sample_sheet_download(self, set_euid: str) -> tuple[str, str, str]:
         run_set = self._require(set_euid)
@@ -999,7 +1032,11 @@ def sequencing_sample_sheet_download(self, set_euid: str) -> tuple[str, str, str
         content = self.sequencing_sample_sheet(set_euid)
         if platform == "ONT":
             return content, f"{set_euid}_ONT_manifest.tsv", "text/tab-separated-values"
-        return content, f"{set_euid}_{platform or 'sequencing'}_SampleSheet.csv", "text/csv"
+        return (
+            content,
+            f"{set_euid}_{platform or 'sequencing'}_SampleSheet.csv",
+            "text/csv",
+        )
 
     def _illumina_sample_sheet(
         self, *, run_set, props: dict[str, Any], data_rows: list[dict[str, str]]
@@ -1042,7 +1079,9 @@ def _ont_sample_sheet(
                     "alias": row.get("Sample_Name") or row.get("Sample_ID") or "",
                     "barcode": row.get("index") or "",
                     "run_set_euid": run_set.euid,
-                    "library_euid": description.get("library_euid") or row.get("Sample_ID") or "",
+                    "library_euid": description.get("library_euid")
+                    or row.get("Sample_ID")
+                    or "",
                     "source_gdna_euid": description.get("source_gdna_euid") or "",
                     "source_specimen_content_euid": description.get(
                         "source_specimen_content_euid"
@@ -1081,7 +1120,10 @@ def _sheet_action(self, sheet: ParsedSheet) -> str:
                 return "seq_run_set"
             if {"input_euid", "input_euids"} & headers:
                 return "seq_pool"
-            if "source_well_euid" in headers and {"index_barcode", "index_euid"} & headers:
+            if (
+                "source_well_euid" in headers
+                and {"index_barcode", "index_euid"} & headers
+            ):
                 return "seq_library_plate"
             if {"source_well_euid", "qc_row", "qc_col"} & headers:
                 return "extraction_qc"
@@ -1104,12 +1146,18 @@ def _sheet_action(self, sheet: ParsedSheet) -> str:
         if name in {"sets", "set", "run sets", "run set"}:
             return "sets"
         if name in {"plate well data", "well data", "annotation"}:
-            return "plate_well_data" if name != "annotation" else "container_annotation_preview"
+            return (
+                "plate_well_data"
+                if name != "annotation"
+                else "container_annotation_preview"
+            )
         if name in {"bulk create", "transfer"}:
             return "container_interaction_preview"
         return "unknown"
 
-    def _request_from_extraction_sheet(self, sheet: ParsedSheet) -> ExtractionPlateRequest:
+    def _request_from_extraction_sheet(
+        self, sheet: ParsedSheet
+    ) -> ExtractionPlateRequest:
         assignments: list[ExtractionTubeAssignment] = []
         tube_euids: list[str] = []
         plate_name: str | None = None
@@ -1120,8 +1168,14 @@ def _request_from_extraction_sheet(self, sheet: ParsedSheet) -> ExtractionPlateR
             if not tube_euid:
                 continue
             plate_name = plate_name or str(row.get("plate_name") or "").strip() or None
-            row_name = row.get("row") or row.get("well_row") or row.get("child_container_row")
-            col_value = row.get("col") or row.get("well_col") or row.get("child_container_column")
+            row_name = (
+                row.get("row") or row.get("well_row") or row.get("child_container_row")
+            )
+            col_value = (
+                row.get("col")
+                or row.get("well_col")
+                or row.get("child_container_column")
+            )
             if row_name not in (None, "") or col_value not in (None, ""):
                 assignments.append(
                     ExtractionTubeAssignment(
@@ -1150,13 +1204,21 @@ def _request_from_qc_sheet(self, sheet: ParsedSheet) -> ExtractionQcPlateRequest
         qc_plate_name = None
         assignments: list[ExtractionQcAssignment] = []
         for row in sheet.rows:
-            source_plate_euid = source_plate_euid or str(
-                row.get("source_plate_euid") or row.get("plate_euid") or ""
-            ).strip() or None
-            qc_plate_name = qc_plate_name or str(row.get("qc_plate_name") or "").strip() or None
+            source_plate_euid = (
+                source_plate_euid
+                or str(
+                    row.get("source_plate_euid") or row.get("plate_euid") or ""
+                ).strip()
+                or None
+            )
+            qc_plate_name = (
+                qc_plate_name or str(row.get("qc_plate_name") or "").strip() or None
+            )
             assignments.append(
                 ExtractionQcAssignment(
-                    source_well_euid=str(row.get("source_well_euid") or row.get("well_euid") or "").strip()
+                    source_well_euid=str(
+                        row.get("source_well_euid") or row.get("well_euid") or ""
+                    ).strip()
                     or None,
                     row=row.get("row") or row.get("well_row"),
                     col=row.get("col") or row.get("well_col"),
@@ -1178,18 +1240,23 @@ def _request_from_library_sheet(self, sheet: ParsedSheet) -> SeqLibraryPlateRequ
         plate_name = None
         assignments: list[LibraryPlateAssignment] = []
         for row in sheet.rows:
-            source_plate_euid = source_plate_euid or str(
-                row.get("source_plate_euid") or ""
-            ).strip() or None
+            source_plate_euid = (
+                source_plate_euid
+                or str(row.get("source_plate_euid") or "").strip()
+                or None
+            )
             plate_name = plate_name or str(row.get("plate_name") or "").strip() or None
-            source_well_euid = str(row.get("source_well_euid") or row.get("well_euid") or "").strip()
+            source_well_euid = str(
+                row.get("source_well_euid") or row.get("well_euid") or ""
+            ).strip()
             if source_well_euid:
                 assignments.append(
                     LibraryPlateAssignment(
                         source_well_euid=source_well_euid,
                         row=row.get("row") or row.get("well_row"),
                         col=row.get("col") or row.get("well_col"),
-                        index_barcode=str(row.get("index_barcode") or "").strip() or None,
+                        index_barcode=str(row.get("index_barcode") or "").strip()
+                        or None,
                         index_euid=str(row.get("index_euid") or "").strip() or None,
                         data=self._row_metadata(row, "data_", "library_"),
                     )
@@ -1224,7 +1291,9 @@ def _request_from_pool_sheet(self, sheet: ParsedSheet) -> SeqLibraryPoolRequest:
                 )
             )
             platform = str(row.get("platform") or platform).strip() or platform
-            pool_tube_euid = pool_tube_euid or str(row.get("pool_tube_euid") or "").strip() or None
+            pool_tube_euid = (
+                pool_tube_euid or str(row.get("pool_tube_euid") or "").strip() or None
+            )
             pool_name = pool_name or str(row.get("pool_name") or "").strip() or None
             metadata.update(self._row_metadata(row, "metadata_", "pool_"))
         return SeqLibraryPoolRequest(
@@ -1246,8 +1315,12 @@ def _request_from_run_sheet(self, sheet: ParsedSheet) -> SeqRunSetRequest:
             operator=str(row.get("operator") or "").strip() or None,
             instrument_euid=str(row.get("instrument_euid") or "").strip() or None,
             machine=str(row.get("machine") or "").strip() or None,
-            flowcell_barcode=str(row.get("flowcell_barcode") or row.get("flowcell") or "").strip(),
-            reagent_euids=self._split_values(row.get("reagent_euids") or row.get("reagents")),
+            flowcell_barcode=str(
+                row.get("flowcell_barcode") or row.get("flowcell") or ""
+            ).strip(),
+            reagent_euids=self._split_values(
+                row.get("reagent_euids") or row.get("reagents")
+            ),
             status=str(row.get("status") or "created").strip() or "created",
             name=str(row.get("name") or "").strip() or None,
             description=str(row.get("description") or "").strip() or None,
@@ -1264,16 +1337,28 @@ def _request_from_data_sheet(self, sheet: ParsedSheet) -> PlateWellDataRequest:
                 or row.get("annotation_template_euid")
                 or data_template_code
             ).strip()
-            relationship_type = str(row.get("relationship_type") or relationship_type).strip()
+            relationship_type = str(
+                row.get("relationship_type") or relationship_type
+            ).strip()
             records.append(
                 PlateWellDataRecord(
-                    well_euid=str(row.get("well_euid") or row.get("child_container_euid") or "").strip()
+                    well_euid=str(
+                        row.get("well_euid") or row.get("child_container_euid") or ""
+                    ).strip()
                     or None,
-                    plate_euid=str(row.get("plate_euid") or row.get("container_euid") or "").strip()
+                    plate_euid=str(
+                        row.get("plate_euid") or row.get("container_euid") or ""
+                    ).strip()
                     or None,
-                    row=row.get("row") or row.get("well_row") or row.get("child_container_row"),
-                    col=row.get("col") or row.get("well_col") or row.get("child_container_column"),
-                    name=str(row.get("name") or row.get("annotation_name") or "").strip()
+                    row=row.get("row")
+                    or row.get("well_row")
+                    or row.get("child_container_row"),
+                    col=row.get("col")
+                    or row.get("well_col")
+                    or row.get("child_container_column"),
+                    name=str(
+                        row.get("name") or row.get("annotation_name") or ""
+                    ).strip()
                     or None,
                     target="content"
                     if "content"
@@ -1281,11 +1366,17 @@ def _request_from_data_sheet(self, sheet: ParsedSheet) -> PlateWellDataRequest:
                         row.get("target")
                         or row.get("annotate_container_child_container_content")
                         or "content"
-                    ).strip().lower()
+                    )
+                    .strip()
+                    .lower()
                     else "well",
                     data={
                         **self._row_metadata(row, "data_", "annotation_", "metric_"),
-                        **({"value": row.get("annotation_value")} if row.get("annotation_value") not in (None, "") else {}),
+                        **(
+                            {"value": row.get("annotation_value")}
+                            if row.get("annotation_value") not in (None, "")
+                            else {}
+                        ),
                     },
                 )
             )
@@ -1305,13 +1396,21 @@ def _requests_from_sets_sheet(self, sheet: ParsedSheet) -> list[LabSetRequest]:
                 LabSetRequest(
                     name=name,
                     description=str(row.get("description") or "").strip() or None,
-                    members=self._split_values(row.get("members") or row.get("member_euids")),
+                    members=self._split_values(
+                        row.get("members") or row.get("member_euids")
+                    ),
                     external_members=self._split_values(row.get("external_members")),
                     operator=str(row.get("operator") or "").strip() or None,
-                    instrument=str(row.get("instrument") or row.get("instrument_euid") or "").strip() or None,
-                    reagents=self._split_values(row.get("reagents") or row.get("reagent_euids")),
+                    instrument=str(
+                        row.get("instrument") or row.get("instrument_euid") or ""
+                    ).strip()
+                    or None,
+                    reagents=self._split_values(
+                        row.get("reagents") or row.get("reagent_euids")
+                    ),
                     machine=str(row.get("machine") or "").strip() or None,
-                    flowcell_barcode=str(row.get("flowcell_barcode") or "").strip() or None,
+                    flowcell_barcode=str(row.get("flowcell_barcode") or "").strip()
+                    or None,
                     status=str(row.get("status") or "created").strip() or "created",
                     metadata=self._row_metadata(row, "metadata_", "set_"),
                 )
@@ -1331,7 +1430,11 @@ def import_spreadsheet(
                 "headers": sheet.headers,
                 "row_count": len(sheet.rows),
             }
-            if action in {"container_interaction_preview", "container_annotation_preview", "unknown"}:
+            if action in {
+                "container_interaction_preview",
+                "container_annotation_preview",
+                "unknown",
+            }:
                 entry["preview_rows"] = sheet.rows[:25]
                 actions.append(entry)
                 continue
@@ -1399,4 +1502,8 @@ def print_euids(self, request: PrintEuidRequest) -> dict[str, Any]:
                     print_n=request.copies,
                 )
             )
-        return {"printed": 0 if request.dry_run else len(results), "dry_run": request.dry_run, "results": results}
+        return {
+            "printed": 0 if request.dry_run else len(results),
+            "dry_run": request.dry_run,
+            "results": results,
+        }
diff --git a/bloom_lims/etc/prefix_ownership_registry.json b/bloom_lims/etc/prefix_ownership_registry.json
index 2acba7a..9c703fd 100644
--- a/bloom_lims/etc/prefix_ownership_registry.json
+++ b/bloom_lims/etc/prefix_ownership_registry.json
@@ -172,6 +172,9 @@
       "GVR": {
         "issuer_app_code": "daylily-tapdb"
       },
+      "GSE": {
+        "issuer_app_code": "daylily-tapdb"
+      },
       "MSG": {
         "issuer_app_code": "daylily-tapdb"
       },
diff --git a/bloom_lims/gui/actions.py b/bloom_lims/gui/actions.py
index a41d394..d695dd2 100644
--- a/bloom_lims/gui/actions.py
+++ b/bloom_lims/gui/actions.py
@@ -25,10 +25,19 @@
     {"value": "beta_pool_member", "label": "beta_pool_member"},
     {"value": "beta_pooling_run_input", "label": "beta_pooling_run_input"},
     {"value": "beta_sequencing_run", "label": "beta_sequencing_run"},
-    {"value": "beta_sequenced_library_assignment", "label": "beta_sequenced_library_assignment"},
+    {
+        "value": "beta_sequenced_library_assignment",
+        "label": "beta_sequenced_library_assignment",
+    },
     {"value": "beta_assignment_source", "label": "beta_assignment_source"},
-    {"value": "beta_assignment_library_material", "label": "beta_assignment_library_material"},
-    {"value": "beta_assignment_barcode_reagent", "label": "beta_assignment_barcode_reagent"},
+    {
+        "value": "beta_assignment_library_material",
+        "label": "beta_assignment_library_material",
+    },
+    {
+        "value": "beta_assignment_barcode_reagent",
+        "label": "beta_assignment_barcode_reagent",
+    },
     {"value": "beta_run_artifact", "label": "beta_run_artifact"},
 ]
 
diff --git a/bloom_lims/integrations/tapdb_mount.py b/bloom_lims/integrations/tapdb_mount.py
index e81f39e..4ed417e 100644
--- a/bloom_lims/integrations/tapdb_mount.py
+++ b/bloom_lims/integrations/tapdb_mount.py
@@ -112,7 +112,9 @@ def _build_tapdb_host_bridge() -> TapdbHostBridge:
         shell_title="Bloom",
         shell_subtitle="TapDB substrate",
         home_url="/",
-        login_url=lambda request: f"/login?next={quote(_request_next_path(request), safe='/')}",
+        login_url=lambda request: (
+            f"/login?next={quote(_request_next_path(request), safe='/')}"
+        ),
         logout_url="/logout",
         change_password_url=None,
         resolve_user=_tapdb_host_user,
diff --git a/bloom_lims/schemas/beta_lab.py b/bloom_lims/schemas/beta_lab.py
index 1e855ea..1cbe634 100644
--- a/bloom_lims/schemas/beta_lab.py
+++ b/bloom_lims/schemas/beta_lab.py
@@ -101,7 +101,9 @@ def validate_context(self) -> "AtlasFulfillmentContext":
         self.atlas_order_test_euids = normalized_order_test_euids
         if self.atlas_order_test_euid is None and self.atlas_order_test_euids:
             self.atlas_order_test_euid = self.atlas_order_test_euids[0]
-        if (self.atlas_order_test_euid or self.atlas_order_test_euids) and not self.atlas_order_euid:
+        if (
+            self.atlas_order_test_euid or self.atlas_order_test_euids
+        ) and not self.atlas_order_euid:
             raise ValueError(
                 "atlas_order_euid is required when atlas_order_test_euid is provided"
             )
@@ -394,9 +396,9 @@ class BetaRunArtifactInput(BaseModel):
 class BetaRunCreateRequest(BaseModel):
     pool_euid: str
     platform: Literal["ILMN", "ONT", "Ultima", "PacBio", "CompleteGenomics"]
-    run_subtype: Literal[
-        "illumina", "ont", "ultima", "pacbio", "completegenomics"
-    ] = Field(default="illumina")
+    run_subtype: Literal["illumina", "ont", "ultima", "pacbio", "completegenomics"] = (
+        Field(default="illumina")
+    )
     flowcell_id: str
     run_name: str | None = None
     status: Literal["started", "completed"] = Field(default="completed")
diff --git a/bloom_lims/schemas/lab_actions.py b/bloom_lims/schemas/lab_actions.py
index 9757601..bb0b283 100644
--- a/bloom_lims/schemas/lab_actions.py
+++ b/bloom_lims/schemas/lab_actions.py
@@ -172,7 +172,9 @@ class PlateWellDataRecord(BaseModel):
 
     @model_validator(mode="after")
     def validate_target(self) -> "PlateWellDataRecord":
-        if self.well_euid and (self.plate_euid or self.row is not None or self.col is not None):
+        if self.well_euid and (
+            self.plate_euid or self.row is not None or self.col is not None
+        ):
             raise ValueError("provide well_euid or plate_euid with row/col, not both")
         if not self.well_euid:
             if not self.plate_euid or self.row is None or self.col is None:
diff --git a/bloom_lims/schemas/objects.py b/bloom_lims/schemas/objects.py
index deb3d97..784fdb4 100644
--- a/bloom_lims/schemas/objects.py
+++ b/bloom_lims/schemas/objects.py
@@ -21,7 +21,9 @@ class JsonAddlSchema(BloomBaseSchema):
     # Common optional fields
     notes: Optional[str] = Field(None, max_length=10000, description="General notes")
     tags: Optional[List[str]] = Field(None, description="Tags for categorization")
-    custom_fields: Optional[Dict[str, Any]] = Field(None, description="Custom field values")
+    custom_fields: Optional[Dict[str, Any]] = Field(
+        None, description="Custom field values"
+    )
 
     # Allow extra fields for flexibility
     model_config = {"extra": "allow"}
@@ -41,10 +43,19 @@ class ObjectBaseSchema(BloomBaseSchema):
     """Base schema for BloomObj/generic_instance objects."""
 
     name: str = Field(..., min_length=1, max_length=500, description="Object name")
-    type: str = Field(..., min_length=1, max_length=100, description="Object type (e.g., sample, plate)")
+    type: str = Field(
+        ...,
+        min_length=1,
+        max_length=100,
+        description="Object type (e.g., sample, plate)",
+    )
     subtype: Optional[str] = Field(None, max_length=100, description="Object subtype")
-    category: str = Field(default="instance", max_length=50, description="Object category")
-    json_addl: Optional[Dict[str, Any]] = Field(default_factory=dict, description="Additional JSON data")
+    category: str = Field(
+        default="instance", max_length=50, description="Object category"
+    )
+    json_addl: Optional[Dict[str, Any]] = Field(
+        default_factory=dict, description="Additional JSON data"
+    )
 
     @field_validator("type", mode="before")
     @classmethod
@@ -62,6 +73,7 @@ def ensure_json_addl_dict(cls, v):
             return {}
         if isinstance(v, str):
             import json
+
             try:
                 return json.loads(v)
             except json.JSONDecodeError:
@@ -72,10 +84,16 @@ def ensure_json_addl_dict(cls, v):
 class ObjectCreateSchema(ObjectBaseSchema):
     """Schema for creating a new BloomObj."""
 
-    parent_euid: Optional[str] = Field(None, description="Parent object EUID for lineage")
+    parent_euid: Optional[str] = Field(
+        None, description="Parent object EUID for lineage"
+    )
     lineage_euid: Optional[str] = Field(None, description="Lineage EUID to attach to")
-    container_euid: Optional[str] = Field(None, description="Container EUID for placement")
-    container_position: Optional[str] = Field(None, description="Position in container (e.g., A1)")
+    container_euid: Optional[str] = Field(
+        None, description="Container EUID for placement"
+    )
+    container_position: Optional[str] = Field(
+        None, description="Position in container (e.g., A1)"
+    )
     count: int = Field(
         default=1,
         ge=1,
@@ -95,16 +113,30 @@ def validate_euids(cls, v):
 class ObjectUpdateSchema(BloomBaseSchema):
     """Schema for updating an existing BloomObj."""
 
-    name: Optional[str] = Field(None, min_length=1, max_length=500, description="Object name")
-    json_addl: Optional[Dict[str, Any]] = Field(None, description="Additional JSON data (merged)")
+    name: Optional[str] = Field(
+        None, min_length=1, max_length=500, description="Object name"
+    )
+    json_addl: Optional[Dict[str, Any]] = Field(
+        None, description="Additional JSON data (merged)"
+    )
     status: Optional[str] = Field(None, max_length=50, description="Object status")
     is_deleted: Optional[bool] = Field(None, description="Soft delete flag")
-    created_dt: Optional[datetime] = Field(None, description="Creation datetime (admin only)")
+    created_dt: Optional[datetime] = Field(
+        None, description="Creation datetime (admin only)"
+    )
 
     @model_validator(mode="after")
     def check_at_least_one_field(self):
         """Ensure at least one field is provided for update."""
-        if not any([self.name, self.json_addl, self.status, self.is_deleted is not None, self.created_dt]):
+        if not any(
+            [
+                self.name,
+                self.json_addl,
+                self.status,
+                self.is_deleted is not None,
+                self.created_dt,
+            ]
+        ):
             raise ValueError("At least one field must be provided for update")
         return self
 
@@ -116,7 +148,9 @@ class ObjectResponseSchema(ObjectBaseSchema, TimestampMixin):
     status: str = Field(default="active", description="Object status")
     is_deleted: bool = Field(default=False, description="Soft delete flag")
     is_singleton: bool = Field(default=False, description="Singleton instance flag")
-    polymorphic_discriminator: Optional[str] = Field(None, description="Type discriminator")
+    polymorphic_discriminator: Optional[str] = Field(
+        None, description="Type discriminator"
+    )
 
     # Relationship info (optional)
     parent_euid: Optional[str] = Field(None, description="Parent object EUID")
@@ -136,9 +170,15 @@ class ObjectQueryParams(BloomBaseSchema):
     parent_euid: Optional[str] = Field(None, description="Filter by parent")
     lineage_euid: Optional[str] = Field(None, description="Filter by lineage")
     container_euid: Optional[str] = Field(None, description="Filter by container")
-    created_after: Optional[datetime] = Field(None, description="Filter by creation date")
-    created_before: Optional[datetime] = Field(None, description="Filter by creation date")
-    include_deleted: bool = Field(default=False, description="Include soft-deleted objects")
+    created_after: Optional[datetime] = Field(
+        None, description="Filter by creation date"
+    )
+    created_before: Optional[datetime] = Field(
+        None, description="Filter by creation date"
+    )
+    include_deleted: bool = Field(
+        default=False, description="Include soft-deleted objects"
+    )
 
     @field_validator("type", "subtype", mode="before")
     @classmethod
diff --git a/bloom_lims/tapdb_metrics.py b/bloom_lims/tapdb_metrics.py
index 2c8be42..a4f4fca 100644
--- a/bloom_lims/tapdb_metrics.py
+++ b/bloom_lims/tapdb_metrics.py
@@ -85,7 +85,9 @@ def _explicit_config_metrics_enabled(config_path: Path) -> bool | None:
     try:
         loaded = yaml.safe_load(config_path.read_text(encoding="utf-8"))
     except yaml.YAMLError as exc:
-        raise RuntimeError(f"Failed to parse Bloom TapDB metrics config: {exc}") from exc
+        raise RuntimeError(
+            f"Failed to parse Bloom TapDB metrics config: {exc}"
+        ) from exc
     if not isinstance(loaded, dict):
         return None
     target = loaded.get("target")
diff --git a/container_tests/test_container_runtime.py b/container_tests/test_container_runtime.py
index 4f93a29..6d8617d 100644
--- a/container_tests/test_container_runtime.py
+++ b/container_tests/test_container_runtime.py
@@ -7,7 +7,6 @@
 
 from bloom_lims import container_entry
 
-
 PROJECT_ROOT = Path(__file__).resolve().parents[1]
 
 
@@ -18,7 +17,7 @@ def test_docker_runtime_files_use_foreground_uv_and_no_legacy_runtime() -> None:
     assert "uv sync --frozen --no-dev --no-install-project" in dockerfile
     assert "uv sync --frozen --no-dev" in dockerfile
     assert "USER lsmc" in dockerfile
-    assert "python\", \"-m\", \"bloom_lims.container_entry" in dockerfile
+    assert 'python", "-m", "bloom_lims.container_entry' in dockerfile
     assert ":latest" not in dockerfile
     assert "conda" not in dockerfile.lower()
     assert "tmux" not in entrypoint
@@ -26,7 +25,9 @@ def test_docker_runtime_files_use_foreground_uv_and_no_legacy_runtime() -> None:
     assert "${BLOOM_CONFIG_PATH:?BLOOM_CONFIG_PATH is required}" in entrypoint
 
 
-def test_container_entry_requires_absolute_config_path(monkeypatch: pytest.MonkeyPatch) -> None:
+def test_container_entry_requires_absolute_config_path(
+    monkeypatch: pytest.MonkeyPatch,
+) -> None:
     monkeypatch.setenv("BLOOM_CONFIG_PATH", "relative.yaml")
 
     with pytest.raises(RuntimeError, match="must be an absolute path"):
diff --git a/pyproject.toml b/pyproject.toml
index 6a6225e..cb87f2a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,8 +28,9 @@ license = {text = "MIT"}
 requires-python = ">=3.12"
 dependencies = [
     "cli-core-yo==2.1.1",
-    "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.9",
+    "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.10",
     "daylily-auth-cognito==2.1.5",
+    "defusedxml>=0.7.1",
     "IPython>=8.18.1",
     "bandit[toml]>=1.8.0",
     "black>=24.0.0",
diff --git a/tests/test_action_button_template_safety.py b/tests/test_action_button_template_safety.py
index b06b0a8..5f3a9bf 100644
--- a/tests/test_action_button_template_safety.py
+++ b/tests/test_action_button_template_safety.py
@@ -2,7 +2,6 @@
 
 from pathlib import Path
 
-
 PROJECT_ROOT = Path(__file__).resolve().parent.parent
 
 
@@ -13,9 +12,12 @@ def _read(path: str) -> str:
 def test_modern_euid_details_uses_data_attribute_action_handler():
     template = _read("templates/modern/euid_details.html")
 
-    assert "onclick=\"showCapturedDataFormFromDataAttributes(this)\"" in template
-    assert "data-action-json=\"{{ action_value | tojson | e }}\"" in template
-    assert "onclick=\"showCapturedDataForm(this, {{ action_value | tojson }}" not in template
+    assert 'onclick="showCapturedDataFormFromDataAttributes(this)"' in template
+    assert 'data-action-json="{{ action_value | tojson | e }}"' in template
+    assert (
+        'onclick="showCapturedDataForm(this, {{ action_value | tojson }}'
+        not in template
+    )
 
 
 def test_modern_euid_details_has_no_toast_only_print_button():
@@ -28,10 +30,13 @@ def test_modern_euid_details_has_no_toast_only_print_button():
 def test_modern_workflow_details_uses_data_attribute_action_handler():
     template = _read("templates/modern/workflow_details.html")
 
-    assert "onclick=\"showCapturedDataFormFromDataAttributes(this)\"" in template
-    assert "data-action-json=\"{{ action_value | tojson | e }}\"" in template
-    assert "onclick=\"showCapturedDataForm(this, {{ action_value }}" not in template
-    assert "onclick=\"showCapturedDataForm(this, {{ action_value | tojson }}" not in template
+    assert 'onclick="showCapturedDataFormFromDataAttributes(this)"' in template
+    assert 'data-action-json="{{ action_value | tojson | e }}"' in template
+    assert 'onclick="showCapturedDataForm(this, {{ action_value }}' not in template
+    assert (
+        'onclick="showCapturedDataForm(this, {{ action_value | tojson }}'
+        not in template
+    )
 
 
 def test_action_buttons_uses_ui_schema_fields_array_for_filtering():
diff --git a/tests/test_action_schema_hydration.py b/tests/test_action_schema_hydration.py
index 2b508d1..b84a45b 100644
--- a/tests/test_action_schema_hydration.py
+++ b/tests/test_action_schema_hydration.py
@@ -74,9 +74,10 @@ def test_hydrate_dynamic_action_groups_adds_relationship_type_dropdown():
     assert {"value": "derived_from", "label": "derived_from"} in relationship_field[
         "options"
     ]
-    assert {"value": "beta_sequencing_run", "label": "beta_sequencing_run"} in relationship_field[
-        "options"
-    ]
+    assert {
+        "value": "beta_sequencing_run",
+        "label": "beta_sequencing_run",
+    } in relationship_field["options"]
 
 
 def test_hydrate_dynamic_action_groups_hides_subject_decision_scope_action():
diff --git a/tests/test_anomalies.py b/tests/test_anomalies.py
index 888b8b3..cc48de9 100644
--- a/tests/test_anomalies.py
+++ b/tests/test_anomalies.py
@@ -33,7 +33,9 @@ def _build_fake_repository() -> TapdbAnomalyRepository:
     instances: list[SimpleNamespace] = []
     counter = {"value": 0}
 
-    def create_instance(*, template_code: str, name: str, properties: dict, session) -> SimpleNamespace:
+    def create_instance(
+        *, template_code: str, name: str, properties: dict, session
+    ) -> SimpleNamespace:
         counter["value"] += 1
         category, type_name, subtype, version = template_code.strip("/").split("/")
         instance = SimpleNamespace(
@@ -174,7 +176,9 @@ def test_anomaly_api_lists_and_reads_records(monkeypatch) -> None:
 
 def test_admin_anomalies_views_render(monkeypatch) -> None:
     monkeypatch.setattr(operations, "BLOOMdb3", _StubBloomDB)
-    monkeypatch.setattr(operations, "TapdbAnomalyRepository", lambda _session: _StubRepository())
+    monkeypatch.setattr(
+        operations, "TapdbAnomalyRepository", lambda _session: _StubRepository()
+    )
 
     with TestClient(app, raise_server_exceptions=False) as client:
         listing = client.get("/admin/anomalies")
diff --git a/tests/test_beta_lab_schema.py b/tests/test_beta_lab_schema.py
index 74dfe1c..1921048 100644
--- a/tests/test_beta_lab_schema.py
+++ b/tests/test_beta_lab_schema.py
@@ -29,7 +29,9 @@ def test_atlas_fulfillment_context_preserves_order_refs():
         "Z-AGX-TEST1",
         "Z-AGX-TEST2",
     ]
-    assert payload["fulfillment_slots"][0]["atlas_fulfillment_slot_euid"] == "Z-AGX-SLOT1"
+    assert (
+        payload["fulfillment_slots"][0]["atlas_fulfillment_slot_euid"] == "Z-AGX-SLOT1"
+    )
 
 
 def test_atlas_fulfillment_context_requires_order_for_order_tests():
diff --git a/tests/test_beta_modern_action_system.py b/tests/test_beta_modern_action_system.py
index 03b4b5c..4f82f03 100644
--- a/tests/test_beta_modern_action_system.py
+++ b/tests/test_beta_modern_action_system.py
@@ -1029,15 +1029,57 @@ def v0_edge_tuples():
             library_material_euid,
             "source_material",
         ),
-        ("RUN_CONSUMED", extraction_body["extraction_run_euid"], "workflow_run", specimen_euid, "consumed_material"),
-        ("RUN_PRODUCED", extraction_body["extraction_run_euid"], "workflow_run", extraction_output_euid, "produced_material"),
-        ("RUN_CONSUMED", pooling_run_euid, "workflow_run", library_material_euid, "consumed_material"),
-        ("RUN_PRODUCED", pooling_run_euid, "workflow_run", pool_euid, "produced_material"),
+        (
+            "RUN_CONSUMED",
+            extraction_body["extraction_run_euid"],
+            "workflow_run",
+            specimen_euid,
+            "consumed_material",
+        ),
+        (
+            "RUN_PRODUCED",
+            extraction_body["extraction_run_euid"],
+            "workflow_run",
+            extraction_output_euid,
+            "produced_material",
+        ),
+        (
+            "RUN_CONSUMED",
+            pooling_run_euid,
+            "workflow_run",
+            library_material_euid,
+            "consumed_material",
+        ),
+        (
+            "RUN_PRODUCED",
+            pooling_run_euid,
+            "workflow_run",
+            pool_euid,
+            "produced_material",
+        ),
         ("RUN_CONSUMED", run_euid, "workflow_run", pool_euid, "consumed_material"),
-        ("RUN_CONSUMED", run_euid, "workflow_run", lib_output_euid, "consumed_artifact"),
-        ("RUN_CONSUMED", run_euid, "workflow_run", library_material_euid, "consumed_material"),
+        (
+            "RUN_CONSUMED",
+            run_euid,
+            "workflow_run",
+            lib_output_euid,
+            "consumed_artifact",
+        ),
+        (
+            "RUN_CONSUMED",
+            run_euid,
+            "workflow_run",
+            library_material_euid,
+            "consumed_material",
+        ),
         ("RUN_PRODUCED", run_euid, "workflow_run", artifact_euid, "produced_artifact"),
-        ("SLOT_SATISFIED_BY", fulfillment_slot_ref, "fulfillment_slot", library_material_euid, "satisfying_bloom_object"),
+        (
+            "SLOT_SATISFIED_BY",
+            fulfillment_slot_ref,
+            "fulfillment_slot",
+            library_material_euid,
+            "satisfying_bloom_object",
+        ),
     }.issubset(v0_edge_tuples())
 
     plate_graph = _props(instance(plate_euid))["graph"]
diff --git a/tests/test_cli_db_command_paths.py b/tests/test_cli_db_command_paths.py
index d9aba92..b93d20d 100644
--- a/tests/test_cli_db_command_paths.py
+++ b/tests/test_cli_db_command_paths.py
@@ -630,6 +630,14 @@ def test_retire_obsolete_template_variants_only_deletes_stale_prefixes() -> None
             "instance_prefix": "BRN",
             "json_addl": {"semantic_category": "data"},
         },
+        {
+            "category": "material",
+            "type": "sample",
+            "subtype": "gdna",
+            "version": "1.0",
+            "instance_prefix": "BNG",
+            "json_addl": {"semantic_category": "content"},
+        },
         {
             "category": "container",
             "type": "tube",
@@ -679,6 +687,16 @@ def test_retire_obsolete_template_variants_only_deletes_stale_prefixes() -> None
         bstatus="active",
         json_addl={"semantic_category": "container"},
     )
+    material_content = SimpleNamespace(
+        domain_code="Z",
+        type="sample",
+        category="material",
+        subtype="gdna",
+        version="1.0",
+        is_deleted=False,
+        bstatus="active",
+        json_addl={"semantic_category": "content"},
+    )
     non_data = SimpleNamespace(
         domain_code="Z",
         type="sequencing_run",
@@ -709,6 +727,7 @@ def all(self):
                 stale_prefix,
                 stale_subtype,
                 stale_container_prefix,
+                material_content,
                 non_data,
             ]
 
@@ -731,7 +750,7 @@ def flush(self):
         domain_code="Z",
     )
 
-    assert retired == 4
+    assert retired == 3
     assert current.is_deleted is False
     assert stale_prefix.is_deleted is True
     assert stale_prefix.bstatus == "retired"
@@ -739,8 +758,8 @@ def flush(self):
     assert stale_subtype.bstatus == "retired"
     assert stale_container_prefix.is_deleted is True
     assert stale_container_prefix.bstatus == "retired"
-    assert non_data.is_deleted is True
-    assert non_data.bstatus == "retired"
+    assert material_content.is_deleted is False
+    assert non_data.is_deleted is False
     assert fake_session.flushed == 1
 
 
diff --git a/tests/test_config_runtime.py b/tests/test_config_runtime.py
index 4e23e87..627a372 100644
--- a/tests/test_config_runtime.py
+++ b/tests/test_config_runtime.py
@@ -348,7 +348,9 @@ def test_create_app_does_not_mount_upload_or_tmp_static_dirs(
     get_settings.cache_clear()
 
     app = create_app()
-    mount_paths = {route.path for route in app.routes}
+    mount_paths = {
+        path for route in app.routes if (path := getattr(route, "path", None))
+    }
 
     assert "/static" in mount_paths
     assert "/templates" in mount_paths
@@ -445,7 +447,7 @@ def test_tapdb_contract_defaults_match_shipped_templates(monkeypatch, tmp_path:
     settings = BloomSettings(storage={"upload_dir": str(tmp_path / "uploads")})
     expected_tapdb_spec = read_pyproject_dependency_spec("daylily-tapdb")
 
-    assert expected_tapdb_spec == "==9.0.4"
+    assert expected_tapdb_spec == "==9.0.10"
     assert assert_tapdb_version()
     assert settings.tapdb.owner_repo_name == DEFAULT_TAPDB_OWNER_REPO_NAME
     assert settings.tapdb.domain_code == DEFAULT_TAPDB_DOMAIN_CODE
@@ -557,6 +559,7 @@ def test_tapdb_contract_defaults_match_shipped_templates(monkeypatch, tmp_path:
         "BWF",
         "BWS",
         "EDG",
+        "GSE",
         "GVR",
         "MSG",
         "SYS",
diff --git a/tests/test_core_validation.py b/tests/test_core_validation.py
index 388e728..eed3cb0 100644
--- a/tests/test_core_validation.py
+++ b/tests/test_core_validation.py
@@ -2,17 +2,26 @@
 Tests for bloom_lims.core.validation module.
 """
 
+import json
+import tempfile
+from pathlib import Path
+
 import pytest
 
+from bloom_lims.core.template_validation import (
+    TemplateDefinition,
+    TemplateValidator,
+    ValidationResult,
+)
 from bloom_lims.core.validation import (
     ValidationError,
     validate_euid,
     validate_json_addl,
-    validate_type,
     validate_not_empty,
     validate_positive_int,
-    validated,
     validate_schema,
+    validate_type,
+    validated,
 )
 
 
@@ -68,17 +77,19 @@ def test_invalid_format_with_leading_zero(self):
         with pytest.raises(ValidationError) as exc_info:
             validate_euid("CX01")
         assert "No leading zeros" in str(exc_info.value)
+
+
 class TestValidateJsonAddl:
     """Tests for validate_json_addl function."""
-    
+
     def test_valid_dict(self):
         """Test validation of valid dict."""
         assert validate_json_addl({"key": "value"}) is True
-    
+
     def test_none_allowed(self):
         """Test that None is allowed."""
         assert validate_json_addl(None) is True
-    
+
     def test_non_dict(self):
         """Test that non-dict raises ValidationError."""
         with pytest.raises(ValidationError) as exc_info:
@@ -91,6 +102,7 @@ class TestValidatedDecorator:
 
     def test_valid_arguments(self):
         """Test that valid arguments pass through."""
+
         @validated(euid=validate_euid)
         def process(euid: str) -> str:
             return f"processed: {euid}"
@@ -100,6 +112,7 @@ def process(euid: str) -> str:
 
     def test_invalid_argument_raises(self):
         """Test that invalid arguments raise ValidationError."""
+
         @validated(euid=validate_euid)
         def process(euid: str) -> str:
             return f"processed: {euid}"
@@ -109,6 +122,7 @@ def process(euid: str) -> str:
 
     def test_multiple_validators(self):
         """Test multiple validators on different arguments."""
+
         @validated(euid=validate_euid, data=validate_json_addl)
         def process(euid: str, data: dict) -> dict:
             return {"euid": euid, "data": data}
@@ -155,16 +169,6 @@ def test_wrong_type(self):
 
 
 # Template Validation Tests
-from bloom_lims.core.template_validation import (
-    TemplateValidator,
-    ValidationResult,
-    TemplateDefinition,
-)
-from pathlib import Path
-import tempfile
-import json
-
-
 class TestValidationResult:
     """Tests for ValidationResult dataclass."""
 
@@ -244,9 +248,7 @@ def test_validate_with_temp_directory(self):
                 "test_workflow": {
                     "1.0": {
                         "singleton": "0",
-                        "action_imports": {
-                            "test_action": "action/generic/test/1.0"
-                        }
+                        "action_imports": {"test_action": "action/generic/test/1.0"},
                     }
                 }
             }
@@ -274,9 +276,7 @@ def test_grouped_action_imports_is_rejected(self):
                     "1.0": {
                         "singleton": "0",
                         "action_imports": {
-                            "default": {
-                                "actions": {"action/generic/test/1.0": {}}
-                            }
+                            "default": {"actions": {"action/generic/test/1.0": {}}}
                         },
                     }
                 }
@@ -313,21 +313,25 @@ class TestValidatorImports:
     def test_import_validation_error(self):
         """Test ValidationError import."""
         from bloom_lims.core.validation import ValidationError
+
         assert ValidationError is not None
 
     def test_import_validate_euid(self):
         """Test validate_euid import."""
         from bloom_lims.core.validation import validate_euid
+
         assert callable(validate_euid)
 
     def test_import_validate_json_addl(self):
         """Test validate_json_addl import."""
         from bloom_lims.core.validation import validate_json_addl
+
         assert callable(validate_json_addl)
 
     def test_import_validated_decorator(self):
         """Test validated decorator import."""
         from bloom_lims.core.validation import validated
+
         assert callable(validated)
 
 
@@ -361,7 +365,6 @@ def test_validate_schema_missing_required(self):
 
     def test_validate_not_empty_with_values(self):
         """Test validate_not_empty with various values."""
-        from bloom_lims.core.validation import validate_not_empty
 
         assert validate_not_empty("hello") is True
         assert validate_not_empty("  test  ") is True
@@ -370,7 +373,7 @@ def test_validate_not_empty_with_values(self):
 
     def test_validate_not_empty_with_empty(self):
         """Test validate_not_empty with empty values."""
-        from bloom_lims.core.validation import validate_not_empty, ValidationError
+        from bloom_lims.core.validation import ValidationError
 
         with pytest.raises(ValidationError):
             validate_not_empty("")
@@ -383,7 +386,6 @@ def test_validate_not_empty_with_empty(self):
 
     def test_validate_positive_int_valid(self):
         """Test validate_positive_int with valid values."""
-        from bloom_lims.core.validation import validate_positive_int
 
         assert validate_positive_int(1) is True
         assert validate_positive_int(100) is True
@@ -391,7 +393,7 @@ def test_validate_positive_int_valid(self):
 
     def test_validate_positive_int_invalid(self):
         """Test validate_positive_int with invalid values."""
-        from bloom_lims.core.validation import validate_positive_int, ValidationError
+        from bloom_lims.core.validation import ValidationError
 
         with pytest.raises(ValidationError):
             validate_positive_int(0)
@@ -410,54 +412,49 @@ def test_validate_euid_with_prefix(self):
 
         # Valid EUIDs require PREFIX (2-3 uppercase letters) + sequence number (no leading zeros)
         # Pattern: [A-Z]{2,3}[1-9][0-9]*$
-        assert validate_euid("CX1") == True
-        assert validate_euid("WF123") == True
-        assert validate_euid("MRX42") == True
+        assert validate_euid("CX1") is True
+        assert validate_euid("WF123") is True
+        assert validate_euid("MRX42") is True
 
     def test_validate_json_addl_with_dict(self):
         """Test validate_json_addl with dictionary."""
         from bloom_lims.core.validation import validate_json_addl
 
         # Valid dict should pass
-        assert validate_json_addl({"key": "value"}) == True
-        assert validate_json_addl({}) == True
+        assert validate_json_addl({"key": "value"}) is True
+        assert validate_json_addl({}) is True
 
     def test_validate_json_addl_with_none(self):
         """Test validate_json_addl with None."""
         from bloom_lims.core.validation import validate_json_addl
 
         # None should be valid (optional field)
-        assert validate_json_addl(None) == True
+        assert validate_json_addl(None) is True
 
     def test_validate_type_container(self):
         """Test validate_type with container type."""
-        from bloom_lims.core.validation import validate_type
 
-        assert validate_type("container") == True
+        assert validate_type("container") is True
 
     def test_validate_type_content(self):
         """Test validate_type with content type."""
-        from bloom_lims.core.validation import validate_type
 
-        assert validate_type("content") == True
+        assert validate_type("content") is True
 
     def test_validate_type_workflow(self):
         """Test validate_type with workflow type."""
-        from bloom_lims.core.validation import validate_type
 
-        assert validate_type("workflow") == True
+        assert validate_type("workflow") is True
 
     def test_validate_not_empty_with_string(self):
         """Test validate_not_empty with non-empty string."""
-        from bloom_lims.core.validation import validate_not_empty
 
-        assert validate_not_empty("test") == True
+        assert validate_not_empty("test") is True
 
     def test_validate_not_empty_with_list(self):
         """Test validate_not_empty with non-empty list."""
-        from bloom_lims.core.validation import validate_not_empty
 
-        assert validate_not_empty([1, 2, 3]) == True
+        assert validate_not_empty([1, 2, 3]) is True
 
     def test_validate_schema_with_valid_data(self):
         """Test validate_schema with valid data."""
@@ -465,7 +462,7 @@ def test_validate_schema_with_valid_data(self):
 
         schema = {
             "name": {"type": str, "required": True},
-            "count": {"type": int, "required": False}
+            "count": {"type": int, "required": False},
         }
         data = {"name": "test", "count": 5}
         errors = validate_schema(data, schema)
@@ -475,9 +472,7 @@ def test_validate_schema_with_missing_required(self):
         """Test validate_schema with missing required field."""
         from bloom_lims.core.validation import validate_schema
 
-        schema = {
-            "name": {"type": str, "required": True}
-        }
+        schema = {"name": {"type": str, "required": True}}
         data = {}
         errors = validate_schema(data, schema)
         assert len(errors) > 0
diff --git a/tests/test_cytoscape_dag.py b/tests/test_cytoscape_dag.py
index aa3429a..5728d5a 100644
--- a/tests/test_cytoscape_dag.py
+++ b/tests/test_cytoscape_dag.py
@@ -13,12 +13,12 @@
     - Graph data structure validation
 """
 
-import pytest
-import json
 import os
-from pathlib import Path
-from unittest.mock import MagicMock, patch, AsyncMock
 from datetime import datetime
+from pathlib import Path
+from unittest.mock import MagicMock, patch
+
+import pytest
 
 from bloom_lims.gui.routes.graph import _build_dag_filename
 
@@ -33,9 +33,7 @@ def test_valid_dag_structure(self):
                 "nodes": [
                     {"data": {"id": "CX1", "euid": "CX1", "obj_type": "container"}}
                 ],
-                "edges": [
-                    {"data": {"source": "CX1", "target": "CX2", "id": "LX1"}}
-                ]
+                "edges": [{"data": {"source": "CX1", "target": "CX2", "id": "LX1"}}],
             }
         }
         assert "elements" in valid_dag
@@ -45,8 +43,15 @@ def test_valid_dag_structure(self):
     def test_node_required_fields(self):
         """Test that nodes have required fields for Cytoscape rendering."""
         required_fields = ["id", "euid", "obj_type"]
-        node = {"data": {"id": "CX123", "euid": "CX123", "obj_type": "container",
-                        "name": "Test", "color": "#8B00FF"}}
+        node = {
+            "data": {
+                "id": "CX123",
+                "euid": "CX123",
+                "obj_type": "container",
+                "name": "Test",
+                "color": "#8B00FF",
+            }
+        }
 
         for field in required_fields:
             assert field in node["data"], f"Missing required field: {field}"
@@ -54,9 +59,15 @@ def test_node_required_fields(self):
     def test_edge_required_fields(self):
         """Test that edges have required fields."""
         required_fields = ["source", "target", "id"]
-        edge = {"data": {"source": "CX1", "target": "CX2", "id": "LX1", 
-                        "relationship_type": "generic"}}
-        
+        edge = {
+            "data": {
+                "source": "CX1",
+                "target": "CX2",
+                "id": "LX1",
+                "relationship_type": "generic",
+            }
+        }
+
         for field in required_fields:
             assert field in edge["data"], f"Missing required field: {field}"
 
@@ -97,23 +108,23 @@ def _detect_cycle(self, existing_edges, source, target):
         """Helper function implementing cycle detection algorithm."""
         if source == target:
             return True
-        
+
         # Build adjacency list
         graph = {}
         for src, tgt in existing_edges:
             if src not in graph:
                 graph[src] = []
             graph[src].append(tgt)
-        
+
         # Add proposed edge temporarily
         if source not in graph:
             graph[source] = []
         graph[source].append(target)
-        
+
         # DFS to detect cycle from target to source
         visited = set()
         stack = [target]
-        
+
         while stack:
             current = stack.pop()
             if current == source:
@@ -123,7 +134,7 @@ def _detect_cycle(self, existing_edges, source, target):
                 for neighbor in graph.get(current, []):
                     if neighbor not in visited:
                         stack.append(neighbor)
-        
+
         return False
 
 
@@ -375,7 +386,7 @@ def test_add_edge_to_graph(self):
                     {"data": {"id": "CX1"}},
                     {"data": {"id": "CX2"}},
                 ],
-                "edges": []
+                "edges": [],
             }
         }
         new_edge = {"data": {"source": "CX1", "target": "CX2", "id": "LX1"}}
@@ -392,20 +403,18 @@ def test_remove_node_removes_connected_edges(self):
                     {"data": {"id": "CX1"}},
                     {"data": {"id": "CX2"}},
                 ],
-                "edges": [
-                    {"data": {"source": "CX1", "target": "CX2", "id": "LX1"}}
-                ]
+                "edges": [{"data": {"source": "CX1", "target": "CX2", "id": "LX1"}}],
             }
         }
 
         # Remove node CX1
         node_to_remove = "CX1"
         graph["elements"]["nodes"] = [
-            n for n in graph["elements"]["nodes"]
-            if n["data"]["id"] != node_to_remove
+            n for n in graph["elements"]["nodes"] if n["data"]["id"] != node_to_remove
         ]
         graph["elements"]["edges"] = [
-            e for e in graph["elements"]["edges"]
+            e
+            for e in graph["elements"]["edges"]
             if e["data"]["source"] != node_to_remove
             and e["data"]["target"] != node_to_remove
         ]
@@ -488,7 +497,7 @@ def mock_request(self):
 
     def test_get_dagv2_returns_empty_when_file_missing(self, mock_request):
         """Test get_dagv2 returns empty structure when file doesn't exist."""
-        with patch('os.path.exists', return_value=False):
+        with patch("os.path.exists", return_value=False):
             # Simulating the endpoint behavior
             dag_fn = mock_request.session["user_data"]["dag_fnv2"]
             dag_data = {"elements": {"nodes": [], "edges": []}}
@@ -511,10 +520,7 @@ def test_delete_object_endpoint_structure(self):
 
     def test_add_new_edge_request_structure(self):
         """Test add_new_edge endpoint request structure."""
-        request_data = {
-            "parent_euid": "CX1",
-            "child_euid": "CX2"
-        }
+        request_data = {"parent_euid": "CX1", "child_euid": "CX2"}
         assert "parent_euid" in request_data
         assert "child_euid" in request_data
 
@@ -530,19 +536,19 @@ def test_all_edge_nodes_exist(self):
                     {"data": {"id": "CX1"}},
                     {"data": {"id": "CX2"}},
                 ],
-                "edges": [
-                    {"data": {"source": "CX1", "target": "CX2", "id": "LX1"}}
-                ]
+                "edges": [{"data": {"source": "CX1", "target": "CX2", "id": "LX1"}}],
             }
         }
 
         node_ids = {n["data"]["id"] for n in graph["elements"]["nodes"]}
 
         for edge in graph["elements"]["edges"]:
-            assert edge["data"]["source"] in node_ids, \
+            assert edge["data"]["source"] in node_ids, (
                 f"Edge source {edge['data']['source']} not in nodes"
-            assert edge["data"]["target"] in node_ids, \
+            )
+            assert edge["data"]["target"] in node_ids, (
                 f"Edge target {edge['data']['target']} not in nodes"
+            )
 
     def test_no_duplicate_node_ids(self):
         """Test that there are no duplicate node IDs."""
@@ -568,8 +574,9 @@ def test_no_duplicate_edge_ids(self):
     def test_valid_euid_format_in_nodes(self):
         """Test that node EUIDs follow valid format."""
         import re
+
         # EUID pattern: 2-3 uppercase letters + sequence number (no leading zeros)
-        euid_pattern = re.compile(r'^[A-Z]{2,3}[1-9][0-9]*$')
+        euid_pattern = re.compile(r"^[A-Z]{2,3}[1-9][0-9]*$")
 
         valid_euids = ["CX1", "CX123", "WX1000", "MRX42"]
         invalid_euids = ["CX01", "cx1", "C1", "BCN-123"]
@@ -628,9 +635,13 @@ def test_fuzzy_search_no_matches(self):
         """Test fuzzy search with no matches."""
         nodes = [{"id": "CX1", "name": "Test", "obj_type": "container"}]
         query = "xyz"
-        matches = [n for n in nodes if query.lower() in n["id"].lower() or
-                   query.lower() in n["name"].lower() or
-                   query.lower() in n["obj_type"].lower()]
+        matches = [
+            n
+            for n in nodes
+            if query.lower() in n["id"].lower()
+            or query.lower() in n["name"].lower()
+            or query.lower() in n["obj_type"].lower()
+        ]
         assert len(matches) == 0
 
 
@@ -664,6 +675,7 @@ def test_layout_data_includes_zoom_pan(self):
     def test_layout_expiration_check(self):
         """Test layout expiration logic (7 days)."""
         import time
+
         max_age_ms = 7 * 24 * 60 * 60 * 1000  # 7 days in milliseconds
         current_time = int(time.time() * 1000)
 
@@ -687,7 +699,7 @@ def test_timestamp_based_click_detection(self):
         clicks = [0, 100, 200]  # timestamps in ms
         click_count = 1
         for i in range(1, len(clicks)):
-            if clicks[i] - clicks[i-1] < click_threshold_ms:
+            if clicks[i] - clicks[i - 1] < click_threshold_ms:
                 click_count += 1
             else:
                 click_count = 1
@@ -702,7 +714,7 @@ def test_click_reset_on_timeout(self):
         clicks = [0, 100, 700]  # 700ms gap resets count
         click_count = 1
         for i in range(1, len(clicks)):
-            if clicks[i] - clicks[i-1] < click_threshold_ms:
+            if clicks[i] - clicks[i - 1] < click_threshold_ms:
                 click_count += 1
             else:
                 click_count = 1
@@ -803,9 +815,13 @@ def test_graph_js_preserves_tapdb_gestures_and_restored_shortcuts(self):
         assert "runNeighborhoodFromNode(node)" in graph_js
         assert "openNodeActionDialog(node.data())" in graph_js
 
-    def test_graph_js_requires_z_for_mouse_wheel_zoom_and_points_arrows_to_parents(self):
+    def test_graph_js_requires_z_for_mouse_wheel_zoom_and_points_arrows_to_parents(
+        self,
+    ):
         graph_js = Path("static/js/graph.js").read_text(encoding="utf-8")
-        template = Path("templates/modern/dag_explorer.html").read_text(encoding="utf-8")
+        template = Path("templates/modern/dag_explorer.html").read_text(
+            encoding="utf-8"
+        )
 
         assert "configureCytoscapeInteractions(container);" in graph_js
         assert 'key === "z"' in graph_js
diff --git a/tests/test_domain_workflows_helpers.py b/tests/test_domain_workflows_helpers.py
index 1402b1f..768e3c6 100644
--- a/tests/test_domain_workflows_helpers.py
+++ b/tests/test_domain_workflows_helpers.py
@@ -9,8 +9,8 @@
     allow_module_level=True,
 )
 
-import bloom_lims.domain.workflows as workflows_mod
-from bloom_lims.domain.workflows import BloomWorkflowStep
+import bloom_lims.domain.workflows as workflows_mod  # noqa: E402
+from bloom_lims.domain.workflows import BloomWorkflowStep  # noqa: E402
 
 
 def _subject() -> BloomWorkflowStep:
@@ -62,7 +62,9 @@ def test_iter_active_child_instances_filters_deleted_and_type():
     s = _subject()
     keep = _obj("KEEP", category="container", type_name="well")
     deleted_lineage = _obj("DEL-LIN", category="container", type_name="well")
-    deleted_child = _obj("DEL-CHILD", category="container", type_name="well", is_deleted=True)
+    deleted_child = _obj(
+        "DEL-CHILD", category="container", type_name="well", is_deleted=True
+    )
     wrong_type = _obj("WRONG", category="container", type_name="plate")
     parent = SimpleNamespace(
         parent_of_lineages=[
@@ -72,7 +74,9 @@ def test_iter_active_child_instances_filters_deleted_and_type():
             _lineage(wrong_type),
         ]
     )
-    found = list(s._iter_active_child_instances(parent, category="container", type_name="well"))
+    found = list(
+        s._iter_active_child_instances(parent, category="container", type_name="well")
+    )
     assert [child.euid for _, child in found] == ["KEEP"]
 
 
@@ -108,7 +112,10 @@ def test_get_workflow_steps_sorts_by_step_number():
 
 def test_default_queue_name_handles_special_tokens():
     s = _subject()
-    assert s._default_queue_name("input-gdna-normalization-eligible") == "Input gDNA Normalization Eligible"
+    assert (
+        s._default_queue_name("input-gdna-normalization-eligible")
+        == "Input gDNA Normalization Eligible"
+    )
     assert s._default_queue_name("ont-novaseq-libprep") == "ONT Novaseq LibPrep"
 
 
@@ -184,16 +191,33 @@ def test_content_helpers_cover_first_active_child_and_occupancy():
 
 def test_get_plate_wells_in_address_order_and_destination_resolution():
     s = _subject()
-    w2 = _obj("W2", category="container", type_name="well", cont_address={"row_idx": "2", "col_idx": "1"})
-    w1 = _obj("W1", category="container", type_name="well", cont_address={"row_idx": "1", "col_idx": "2"})
-    w0 = _obj("W0", category="container", type_name="well", cont_address={"row_idx": "1", "col_idx": "1"})
+    w2 = _obj(
+        "W2",
+        category="container",
+        type_name="well",
+        cont_address={"row_idx": "2", "col_idx": "1"},
+    )
+    w1 = _obj(
+        "W1",
+        category="container",
+        type_name="well",
+        cont_address={"row_idx": "1", "col_idx": "2"},
+    )
+    w0 = _obj(
+        "W0",
+        category="container",
+        type_name="well",
+        cont_address={"row_idx": "1", "col_idx": "1"},
+    )
     plate = _obj("PLATE1", category="container", type_name="plate")
     plate.parent_of_lineages = [_lineage(w2), _lineage(w1), _lineage(w0)]
 
     ordered = s._get_plate_wells_in_address_order(plate)
     assert [well.euid for well in ordered] == ["W0", "W1", "W2"]
 
-    s._resolve_well_by_plate_and_address = lambda plate_euid, addr: _obj(f"{plate_euid}.{addr}")
+    s._resolve_well_by_plate_and_address = lambda plate_euid, addr: _obj(
+        f"{plate_euid}.{addr}"
+    )
     assert s._resolve_destination_well_ref(plate, "B2").euid == "PLATE1.B2"
     assert s._resolve_destination_well_ref(plate, "PLATE1.A1").euid == "PLATE1.A1"
     with pytest.raises(Exception, match="does not target destination plate"):
@@ -207,20 +231,34 @@ def test_parse_mapping_rows_and_quant_rows_validation():
             "mapping_csv_text": "source_ref,destination_ref\nPLATE1.A1,A1\nPLATE1.B1,B1\n"
         }
     }
-    assert s._parse_mapping_rows(mapping_ds) == [("PLATE1.A1", "A1"), ("PLATE1.B1", "B1")]
+    assert s._parse_mapping_rows(mapping_ds) == [
+        ("PLATE1.A1", "A1"),
+        ("PLATE1.B1", "B1"),
+    ]
 
     with pytest.raises(Exception, match="Invalid mapping row"):
-        s._parse_mapping_rows({"captured_data": {"mapping_csv_text": "source_ref,destination_ref\nONLYSOURCE\n"}})
+        s._parse_mapping_rows(
+            {
+                "captured_data": {
+                    "mapping_csv_text": "source_ref,destination_ref\nONLYSOURCE\n"
+                }
+            }
+        )
 
     quant_ds = {
         "captured_data": {
             "quant_csv_text": "plate_euid,well,quant\nPLATE1,A1,1.5\nPLATE1,B1,2.0\n"
         }
     }
-    assert s._parse_quant_rows(quant_ds) == [("PLATE1", "A1", 1.5), ("PLATE1", "B1", 2.0)]
+    assert s._parse_quant_rows(quant_ds) == [
+        ("PLATE1", "A1", 1.5),
+        ("PLATE1", "B1", 2.0),
+    ]
 
     with pytest.raises(Exception, match="Quant value must be float"):
-        s._parse_quant_rows({"captured_data": {"quant_csv_text": "PLATE1,A1,not-a-float\n"}})
+        s._parse_quant_rows(
+            {"captured_data": {"quant_csv_text": "PLATE1,A1,not-a-float\n"}}
+        )
 
 
 def test_get_library_prep_targets_from_properties_or_defaults():
@@ -236,7 +274,9 @@ def test_get_library_prep_targets_from_properties_or_defaults():
     ]
 
     wf_with_string = _obj("WF2", category="workflow")
-    wf_with_string.json_addl["properties"]["library_prep_queue_subtypes"] = "ont-libprep-eligible"
+    wf_with_string.json_addl["properties"]["library_prep_queue_subtypes"] = (
+        "ont-libprep-eligible"
+    )
     assert s._get_library_prep_targets(wf_with_string) == ["ont-libprep-eligible"]
 
     wf_default = _obj("WF3", category="workflow")
@@ -276,7 +316,9 @@ def test_route_instances_to_library_prep_queues_links_each_instance():
 def test_get_or_create_queue_step_returns_existing_without_creation():
     s = _subject()
     existing = _obj("STEP-EXIST", category="workflow_step", subtype="target")
-    s._get_workflow_steps = lambda _wf, subtype=None: [existing] if subtype == "target" else [existing]
+    s._get_workflow_steps = lambda _wf, subtype=None: (
+        [existing] if subtype == "target" else [existing]
+    )
     s.create_instance_by_code = lambda *_args, **_kwargs: _obj("STEP-NEW")
     s.create_generic_instance_lineage_by_euids = lambda *_args, **_kwargs: None
     s.session = SimpleNamespace(commit=lambda: None)
@@ -286,7 +328,9 @@ def test_get_or_create_queue_step_returns_existing_without_creation():
 
 def test_get_or_create_queue_step_creates_new_step_with_incremented_number():
     s = _subject()
-    highest = _obj("STEP-HIGH", category="workflow_step", subtype="other", step_number="4")
+    highest = _obj(
+        "STEP-HIGH", category="workflow_step", subtype="other", step_number="4"
+    )
     call_state = {"count": 0}
 
     def _get_steps(_wf, subtype=None):
@@ -298,11 +342,11 @@ def _get_steps(_wf, subtype=None):
     created = _obj("STEP-NEW", category="workflow_step", subtype="target-queue")
     captured = {"layout": "", "payload": None, "lineage": None}
     s._get_workflow_steps = _get_steps
-    s.create_instance_by_code = (
-        lambda layout, payload: captured.update({"layout": layout, "payload": payload}) or created
+    s.create_instance_by_code = lambda layout, payload: (
+        captured.update({"layout": layout, "payload": payload}) or created
     )
-    s.create_generic_instance_lineage_by_euids = (
-        lambda parent, child: captured.update({"lineage": (parent, child)})
+    s.create_generic_instance_lineage_by_euids = lambda parent, child: captured.update(
+        {"lineage": (parent, child)}
     )
     s.session = SimpleNamespace(commit=lambda: None)
     workflow = _obj("WF1", category="workflow")
@@ -332,7 +376,9 @@ def test_ensure_lineage_skips_existing_and_creates_when_missing():
 
 def test_fill_plate_from_sources_undirected_and_directed_error_paths():
     s = _subject()
-    queue_step = _obj("Q1", category="workflow_step", subtype="input-gdna-normalization-eligible")
+    queue_step = _obj(
+        "Q1", category="workflow_step", subtype="input-gdna-normalization-eligible"
+    )
     plate = _obj("PLATE1", category="container", type_name="plate")
     source1 = _obj("SRC1", category="container", type_name="well")
     source2 = _obj("SRC2", category="container", type_name="well")
@@ -362,7 +408,9 @@ def _resolve(token):
     s._resolve_destination_well_ref = lambda _plate, _dest: dst1
     s._is_well_occupied = lambda _well: True
     with pytest.raises(Exception, match="Destination well already occupied"):
-        s._fill_plate_from_sources(queue_step, plate, ["A1"], directed_mapping=[("A1", "A1")])
+        s._fill_plate_from_sources(
+            queue_step, plate, ["A1"], directed_mapping=[("A1", "A1")]
+        )
 
 
 def test_fill_plate_from_sources_rejects_insufficient_wells():
@@ -377,7 +425,9 @@ def test_fill_plate_from_sources_rejects_insufficient_wells():
     s._is_well_occupied = lambda _well: False
     s._ensure_lineage = lambda *_args, **_kwargs: None
     s._get_first_active_child_content = lambda _instance: None
-    s._create_output_gdna_content = lambda normalized=False: _obj("OUT", category="content", type_name="sample")
+    s._create_output_gdna_content = lambda normalized=False: _obj(
+        "OUT", category="content", type_name="sample"
+    )
 
     with pytest.raises(Exception, match="Not enough available wells"):
         s._fill_plate_from_sources(queue_step, plate, ["A1", "B1"])
@@ -390,7 +440,9 @@ def test_create_output_gdna_content_sets_normalization_flags(monkeypatch):
     touched: list[str] = []
     s.query_template_by_component_v2 = lambda *_args: [template]
     s.create_instances = lambda _template_euid: [[content_obj]]
-    monkeypatch.setattr(workflows_mod, "flag_modified", lambda _obj, field: touched.append(field))
+    monkeypatch.setattr(
+        workflows_mod, "flag_modified", lambda _obj, field: touched.append(field)
+    )
 
     out = s._create_output_gdna_content(normalized=True)
     assert out.euid == "MX1"
diff --git a/tests/test_lab_actions_api.py b/tests/test_lab_actions_api.py
index 616b867..500cd01 100644
--- a/tests/test_lab_actions_api.py
+++ b/tests/test_lab_actions_api.py
@@ -48,7 +48,9 @@ def _create_object(
     return response.json()
 
 
-def _link_material(client: TestClient, *, container_euid: str, content_euid: str) -> None:
+def _link_material(
+    client: TestClient, *, container_euid: str, content_euid: str
+) -> None:
     response = client.post(
         "/api/v1/lineages/",
         json={
@@ -813,7 +815,7 @@ def cell_ref(row_index: int, col_index: int) -> str:
     worksheet = (
         ''
         ''
-        f'{"".join(sheet_rows)}'
+        f"{''.join(sheet_rows)}"
     )
     output = BytesIO()
     with zipfile.ZipFile(output, "w") as archive:
@@ -847,8 +849,7 @@ def test_spreadsheet_import_csv_and_xlsx_preview() -> None:
     client = _client()
     tube, _ = _create_filled_tube(client, suffix="spreadsheet")
     csv_bytes = (
-        "tube_euid,row,col,plate_name\n"
-        f"{tube},A,1,pytest upload extraction plate\n"
+        f"tube_euid,row,col,plate_name\n{tube},A,1,pytest upload extraction plate\n"
     ).encode()
     dry_run = client.post(
         "/api/v1/lab-actions/spreadsheet-import",
@@ -875,9 +876,24 @@ def test_spreadsheet_import_csv_and_xlsx_preview() -> None:
         [
             [],
             [],
-            ["SOURCE CONTAINER(s)", None, None, None, None, None, None, None, None, "DESTINATION CONTAINER(s)"],
+            [
+                "SOURCE CONTAINER(s)",
+                None,
+                None,
+                None,
+                None,
+                None,
+                None,
+                None,
+                None,
+                "DESTINATION CONTAINER(s)",
+            ],
             ["Container EUID", "Container Template EUID", "Continer Cat/Type/Subtype"],
-            ["BCT-EXAMPLE", "container/tube/tube-generic-10ml/1.0", "container/tube/generic"],
+            [
+                "BCT-EXAMPLE",
+                "container/tube/tube-generic-10ml/1.0",
+                "container/tube/generic",
+            ],
         ],
     )
     parsed = parse_workbook("container_interactions.xlsx", workbook)
diff --git a/tests/test_packaging_metadata.py b/tests/test_packaging_metadata.py
index 6051fbf..ea1b0e0 100644
--- a/tests/test_packaging_metadata.py
+++ b/tests/test_packaging_metadata.py
@@ -15,7 +15,10 @@ def test_project_dependencies_pin_release_train_versions() -> None:
 
     assert "cli-core-yo==2.1.1" in dependencies
     assert "daylily-auth-cognito==2.1.5" in dependencies
-    assert "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.9" in dependencies
+    assert (
+        "daylily-tapdb @ git+https://github.com/Daylily-Informatics/daylily-tapdb.git@9.0.10"
+        in dependencies
+    )
     assert "IPython>=8.18.1" in dependencies
     assert "psycopg2-binary==2.9.12" in dependencies
     assert not any(str(dep).startswith("zebra-day") for dep in dependencies)
@@ -48,7 +51,10 @@ def test_dockerfile_uses_package_specific_scm_version() -> None:
         encoding="utf-8"
     )
 
-    assert "ENV SETUPTOOLS_SCM_PRETEND_VERSION=${SETUPTOOLS_SCM_PRETEND_VERSION}" not in dockerfile
+    assert (
+        "ENV SETUPTOOLS_SCM_PRETEND_VERSION=${SETUPTOOLS_SCM_PRETEND_VERSION}"
+        not in dockerfile
+    )
     assert (
         "ENV SETUPTOOLS_SCM_PRETEND_VERSION_FOR_BLOOM_LIMS=${SETUPTOOLS_SCM_PRETEND_VERSION}"
         in dockerfile
diff --git a/tests/test_queue_flow.py b/tests/test_queue_flow.py
index bf67ba7..b989bdd 100644
--- a/tests/test_queue_flow.py
+++ b/tests/test_queue_flow.py
@@ -73,7 +73,10 @@ def _atlas_context_payload() -> dict[str, object]:
         "atlas_tenant_id": _opaque("tenant"),
         "atlas_order_euid": order_euid,
         "atlas_order_test_euid": primary_order_test_euid,
-        "atlas_order_test_euids": [primary_order_test_euid, _opaque("order-test-secondary")],
+        "atlas_order_test_euids": [
+            primary_order_test_euid,
+            _opaque("order-test-secondary"),
+        ],
         "atlas_trf_euid": _opaque("trf"),
         "atlas_test_euid": _opaque("test-primary"),
         "atlas_test_euids": [_opaque("test-secondary")],
diff --git a/tests/test_route_coverage_gaps_api.py b/tests/test_route_coverage_gaps_api.py
index f42f170..4822d5b 100644
--- a/tests/test_route_coverage_gaps_api.py
+++ b/tests/test_route_coverage_gaps_api.py
@@ -113,9 +113,7 @@ def test_object_creation_creates_all_sequencing_run_platform_prefixes(
         assert created["euid"].startswith(f"{domain_code}-{prefix}-")
 
 
-def test_object_creation_plate_creates_96_linked_wells(
-    client: TestClient, bdb
-) -> None:
+def test_object_creation_plate_creates_96_linked_wells(client: TestClient, bdb) -> None:
     created = _create_instance_via_object_creation(
         client,
         category="container",
@@ -140,8 +138,7 @@ def test_object_creation_plate_creates_96_linked_wells(
     )
     wells = [lineage.child_instance for lineage in lineages]
     positions = {
-        ((well.json_addl or {}).get("cont_address") or {}).get("name")
-        for well in wells
+        ((well.json_addl or {}).get("cont_address") or {}).get("name") for well in wells
     }
     assert len(wells) == 96
     assert {well.type for well in wells} == {"well"}
@@ -288,8 +285,16 @@ def test_containers_content_link_layout_and_delete(client: TestClient, bdb) -> N
     )
     assert link_resp.status_code == 200, link_resp.text
     lineage_cls = bdb.Base.classes.generic_instance_lineage
-    parent = bdb.session.query(bdb.Base.classes.generic_instance).filter_by(euid=container_euid).first()
-    child = bdb.session.query(bdb.Base.classes.generic_instance).filter_by(euid=content_euid).first()
+    parent = (
+        bdb.session.query(bdb.Base.classes.generic_instance)
+        .filter_by(euid=container_euid)
+        .first()
+    )
+    child = (
+        bdb.session.query(bdb.Base.classes.generic_instance)
+        .filter_by(euid=content_euid)
+        .first()
+    )
     lineage = (
         bdb.session.query(lineage_cls)
         .filter(
diff --git a/tests/test_route_coverage_gaps_gui.py b/tests/test_route_coverage_gaps_gui.py
index 7829a83..f9dba10 100644
--- a/tests/test_route_coverage_gaps_gui.py
+++ b/tests/test_route_coverage_gaps_gui.py
@@ -41,9 +41,21 @@ def _warm_session(client: TestClient) -> None:
     assert resp.status_code == 200
 
 
-def _get_any_template_euid(bdb) -> str:
+def _get_bloom_creatable_template_euid(bdb) -> str:
     GT = bdb.Base.classes.generic_template
-    row = bdb.session.query(GT).filter(GT.is_deleted.is_(False)).first()
+    row = (
+        bdb.session.query(GT)
+        .filter(
+            GT.domain_code == "Z",
+            GT.category == "container",
+            GT.type == "tube",
+            GT.subtype == "tube-generic-10ml",
+            GT.version == "1.0",
+            GT.instance_prefix == "BCT",
+            GT.is_deleted.is_(False),
+        )
+        .one_or_none()
+    )
     assert row is not None
     return row.euid
 
@@ -216,7 +228,7 @@ def test_user_audit_logs_renders(client: TestClient) -> None:
 
 def test_create_from_template_executes_handler(client: TestClient, bdb) -> None:
     _warm_session(client)
-    template_euid = _get_any_template_euid(bdb)
+    template_euid = _get_bloom_creatable_template_euid(bdb)
     resp = client.get(
         "/create_from_template", params={"euid": template_euid}, follow_redirects=False
     )
@@ -232,7 +244,7 @@ def test_file_set_urls_and_admin_template_routes_are_removed(
     resp = client.get("/file_set_urls", params={"fs_euid": "BFL-NOT-REAL"})
     assert resp.status_code == 404
 
-    template_euid = _get_any_template_euid(bdb)
+    template_euid = _get_bloom_creatable_template_euid(bdb)
     # Admin template editor was retired.
     resp = client.get("/admin_template", params={"euid": template_euid})
     assert resp.status_code == 404
diff --git a/tests/test_sequencing_run_contract.py b/tests/test_sequencing_run_contract.py
index d689d84..0474c54 100644
--- a/tests/test_sequencing_run_contract.py
+++ b/tests/test_sequencing_run_contract.py
@@ -10,7 +10,6 @@
 
 from bloom_lims.schemas.beta_lab import BetaRunCreateRequest
 
-
 PROJECT_ROOT = Path(__file__).resolve().parents[1]
 
 
diff --git a/tests/test_template_instantiation_recursion.py b/tests/test_template_instantiation_recursion.py
index 752c999..19554a5 100644
--- a/tests/test_template_instantiation_recursion.py
+++ b/tests/test_template_instantiation_recursion.py
@@ -54,7 +54,9 @@ def _fake_bloom_obj(templates):
     def get_by_euid(euid):
         return templates_by_euid.get(euid) or created["instances"].get(euid)
 
-    def query_template_by_component_v2(category=None, type=None, subtype=None, version=None):
+    def query_template_by_component_v2(
+        category=None, type=None, subtype=None, version=None
+    ):
         return [
             template
             for template in templates
@@ -133,9 +135,7 @@ def test_create_instances_recurses_nested_instantiation_layouts():
     assert len(parent_rows) == 1
     assert len(child_rows) == 2
     assert {child.type for child in child_rows} == {"well", "material"}
-    lineages = [
-        row for row in obj.session.added if isinstance(row, _FakeLineage)
-    ]
+    lineages = [row for row in obj.session.added if isinstance(row, _FakeLineage)]
     assert [row.relationship_type for row in lineages] == [
         "HOLDS_MATERIAL",
         "contains",
@@ -151,9 +151,7 @@ def test_create_instances_rejects_template_cycles():
         layouts=[
             {
                 "relationship_type": "contains",
-                "child_templates": [
-                    {"template_code": "container/plate/cycle/1.0/"}
-                ],
+                "child_templates": [{"template_code": "container/plate/cycle/1.0/"}],
             }
         ],
     )
@@ -173,9 +171,7 @@ def test_create_instances_enforces_object_count_limit():
         layouts=[
             {
                 "relationship_type": "contains",
-                "child_templates": [
-                    {"template_code": "container/well/child/1.0/"}
-                ],
+                "child_templates": [{"template_code": "container/well/child/1.0/"}],
             }
         ],
     )
diff --git a/uv.lock b/uv.lock
index f1b5a96..d116384 100644
--- a/uv.lock
+++ b/uv.lock
@@ -160,6 +160,7 @@ dependencies = [
     { name = "daylily-auth-cognito" },
     { name = "daylily-carrier-tracking" },
     { name = "daylily-tapdb" },
+    { name = "defusedxml" },
     { name = "djlint" },
     { name = "fastapi" },
     { name = "httpx" },
@@ -200,7 +201,8 @@ requires-dist = [
     { name = "cli-core-yo", specifier = "==2.1.1" },
     { name = "daylily-auth-cognito", specifier = "==2.1.5" },
     { name = "daylily-carrier-tracking", specifier = "==0.5.1" },
-    { name = "daylily-tapdb", git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.9" },
+    { name = "daylily-tapdb", git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.10" },
+    { name = "defusedxml", specifier = ">=0.7.1" },
     { name = "djlint" },
     { name = "fastapi", specifier = ">=0.110.0" },
     { name = "httpx", specifier = ">=0.27.2" },
@@ -704,8 +706,8 @@ wheels = [
 
 [[package]]
 name = "daylily-tapdb"
-version = "9.0.9"
-source = { git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.9#52d5f498dc4751b7e42d346bee2811a14080e5a5" }
+version = "9.0.10"
+source = { git = "https://github.com/Daylily-Informatics/daylily-tapdb.git?rev=9.0.10#12351b832276d35228527c3c9596e5d60e7c7824" }
 dependencies = [
     { name = "cli-core-yo" },
     { name = "jsonschema" },
@@ -728,6 +730,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/05/7f/798705f5296a58ca505d600456748d1be48078eac8a7050d8a98bc9edb89/decorator-5.3.1-py3-none-any.whl", hash = "sha256:f47fe6fdbd2edd623ecfe36875d37aba411624e2670dd395dddae1358689bb3c", size = 10365, upload-time = "2026-05-18T06:03:26.517Z" },
 ]
 
+[[package]]
+name = "defusedxml"
+version = "0.7.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/0f/d5/c66da9b79e5bdb124974bfe172b4daf3c984ebd9c2a06e2b8a4dc7331c72/defusedxml-0.7.1.tar.gz", hash = "sha256:1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69", size = 75520, upload-time = "2021-03-08T10:59:26.269Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/07/6c/aa3f2f849e01cb6a001cd8554a88d4c77c5c1a31c95bdf1cf9301e6d9ef4/defusedxml-0.7.1-py2.py3-none-any.whl", hash = "sha256:a352e7e428770286cc899e2542b6cdaedb2b4953ff269a210103ec58f6198a61", size = 25604, upload-time = "2021-03-08T10:59:24.45Z" },
+]
+
 [[package]]
 name = "distlib"
 version = "0.4.0"